I've run into this problem a few times at my table. I found that the two most effective ways to retain the realism and our perception of character are either to explain it with fluff or make both player skill and character skill important.
Explain it with Fluff
You have to keep in mind that the characters in most parties most likely think in very different ways. Just because the barbarian can't understand the theories the wizard spouts off doesn't necessarily mean that he's dumb. In fact, his hard lifestyle might have made him a lot more practical at solving practical problems than the wizard who has been shut up in his study for the past who knows how many years. Similarly, even though the dwarf may only have an INT score of 8, he's spent his life working stone, he has a knowledge base that nobody else in the party does. Perhaps you can explain the characters sudden epiphany with one of these devices.
If you really know your group well, you might know their particular puzzle solving strengths. In that case, make the puzzle you intend for them to solve have a theme their character might know about. This takes a very good knowledge of your players but if you can pull it off, everyone will stay immersed and nobody will every be the wiser towards your cunning ruse.
Combining Character Talents and Player Skill
If you enjoy using mechanics more than fluff to solve this problem, consider making these riddles a partial skill challenge. While posing the question, make sure to give some fairly obvious hints that knowledge in certain skills may prove useful to finding the solution. For example, maybe a riddle has an allusion to some hero in the lore that only the bard with his expertise in history would know. Once he catches on and makes a history check, you can tell him some information from the story that makes the answer much easier to find. If you want to make it a particularly hard challenge, make it so that multiple of these hidden clues have to be discovered so that the players can figure out the puzzle.
In the end, if none of these work, it isn't a massive problem. Sure it didn't make much sense as far as characters go, but the plot is advancing and everyone will soon get into the proper mindset again. It's far worse to make a barrier to plot advancement than to see one easily overcome by the wits of your players.
First, it's good if you can find out why the player is playing a non-magic user. You found out it matches his character, which is good, but it might be good to find out what type of gameplay he likes, so you know what to provide and what not to avoid, which might be tricky if you yourself always prefer to player magic-using characters.
Some reasons players might avoid magic-using PC's include:
They don't easily relate to magic powers, and are more interested in non-magic human experiences and situations.
They don't know how the magic system works, and don't want to have to figure out the complexities of it.
They are interested in some other aspect of play (say, detailed combat), and want to focus their skills on that so it will be more interesting and/or their character will be better at fighting.
It's good to know if the reasons are like the above in that there is disinterest in magic, because if so, it may not help to offer them, say, magic items, or a special kind of super power, or even unrealistic martial arts abilities, if they are similar to the things the players don't like about magic, that had them choose to be non-magic users.
In general, I think if a player chooses to be a non-magic fighter type, they will probably appreciate being given interesting combat situations where their character is valuable. Fortunately, you're playing GURPS, which is the best system I know for that. Use tactical combat with a map, and include foes the fencer will be useful against, and/or more (or more resistant) foes than the magic will be able to take care of.
There are other reasons players might choose non-magic-using PCs, which do invite adding magic or magic-like abilities:
A player might have a super-skilled fighter concept, and enjoy meeting a master trainer who can teach them super fighting skills, which may be somewhat magic-like. These can offer not just fighting skills, but skills such as extreme abilities in hiding, jumping, climbing, silent movement, chi powers, possibly magic resistance through will/meditation/chi, and so on. Probably the best source for this sort of thing in GURPS is GURPS Martial Arts.
A player may not want to cast spells, but might like having/using magic items. If there are enough of magic items available that are useful for non-casters, and the groups gives enough of them to the non-fighter PC, then that can give that PC abilities the others don't have.
There may be other types of super powers available in your world that are appropriate to the non-magic-user PC, such as religious-based powers, or psychic powers, or super powers, or whatever. If the player is interested, those can give the player abilities that the magic-users don't have.
In many games, there is so much common magic and magic-like abilities, and they are so useful and/or powerful, that PCs who avoid magic are just going to be much less powerful than those who do. Fortunately, GURPS isn't one of those unless the setting or magic system used makes magic very common and strong. Standard GURPS Magic is quite strong and if most or all of the spells are available and common, there is a lot they can do, but there are still good niches for good fighters.
Another approach can be to have the adversary NPCs notice if/when the players defeat their minions or some situation/puzzle with a conspicuous use of magic. The adversary NPCs may then try to use that knowledge against the party, and come up with ways to challenge the party that counter the magic they know the party has. Something that looks like it can be burned, but can't, to bait and use up the magic of the pyromancer, for example. This can create a situation where the party needs to fight, and the fighters get a chance to shine.
Similarly, you can study the non-magic-user PCs and see what abilities and knowledge they have that are outside the domains of the magic users, and let the PC get chances to notice those. In your case, the sailing thing comes to mind. If he's the only one with seamanship and they're on a ship, he'll have advantages in knowledge, getting around the ship, not getting seasick, and avoiding DX penalties for a rocking deck, etc.
Having studied the PC's abilities, especially when (as you wrote) the player is not as familiar with the game system as you are, you may want to give that player extra information and prompts and ideas throughout the game, based on those abilities, because there are things the PC might think of that the player may not, and this can help the player grow familiar with the opportunities their skills offer.
There may also be places or factions in your campaign setting, who are opposed to magic, or certain types of magic, so that it may be criminal or at least attract attention of ill will if people know you use that magic.
GURPS-specific tips:
Always use a hex map. This makes combats more interesting for fighters, and results in more situations where fighters are needed and useful, and casters have more difficulties, due to range, obstacles, being engaged by attackers, etc. When you're using all the rules, including range penalties and casting times, it often isn't actually all that superior to be a mage in GURPS, as it may take too long to cast a spell, or the target may be too far away, or there may be obstacles to line of sight, or someone may come grapple you, etc.
Get GURPS Swashbucklers for some realistic & cinematic fencing-related abilities, tricks and equipment, as well as some sailing-related stuff.
Have situations where the characters have several challenges with not a whole lot of time to rest in between. In GURPS Magic, the magic-users use up mana when they cast spells, and so they'll need to use it sparingly, or run out of mana by the time they get to the later situations. Meanwhile, the fighters tend to be able to do more per fatigue point. The party may even realize that it needs to save mana for healing and even to restore fatigue on the fighters, if it is to overcome a series of challenges without running out of mana to cast spells.
There are situations in GURPS that call for fencers, such as multiple attackers, or dangerous foes who attack multiple times per turn and are best parried, or that are best disarmed.
GURPS has the concept of Low Mana and No Mana zones, and Aspected Mana Zones and so on, which can also take the magic users down a notch in some places.
Best Answer
The reason the rolls seems unfair is a problem called Goblin Dice.
When talking about combat, d20 decide if a goblin lives or dies - but we all know sooner or later he will kick the bucket.
When we use d20 to determine the success of one-of-a-kind events (like making a bluff check, a diplomacy check or a riddle-solving check), the high variability of the dice makes it for the bad results you named in your comment: "a really smart character rolls a terrible number and unfairly loses the challenge".
This can be solved by rolling several d20, akin to how D&D 4e manages Skill Challenges.
Asking for several intelligence checks and having the puzzle solved when at least N rolls are successful introduces a bell curve in the results, making each single roll less important and less able to influence the results. Smarter characters get less chances to botch all the rolls; dumber characters get less chances to win by pure luck.
The exact number of total rolls and needed successes determines the probability of having the smart character fail or the uneducated character go "Eureka!".
One way to have players work for their result despite only working on the character's skill is turning the series of rolls into a tactical exercise (like "you can choose to have this roll count as a loss and get a +2 to all following rolls").
A second method involves having players consider their character's intelligence. This is obviously prone to metagaming and harder for the not-so-smart-guy-playing-a-wizard.
Seriously? Don't.
Included for completeness, some ideas that involve player and character skill in different ratios:
Note: Goblin Dice as a name was born on Magician's blog