Stealth is fun.
Shadowdancer may be one of the most popular Prestige Classes in 3.5e, and that is solely due to the Hide in Plain Sight feat. Many players enjoy the thought of sneaking invisibly to the enemy and rolling insane backstab/sneak attack damage.
Unfortunately, stealth in D&D is not always that fun.
Now, the backstab part is awesome, and that's why most stealth players enjoy it. The problem is that the D&D mechanics as they are played out in most campaigns do not make much of stealth beyond a canned skill challenge. By looking at some good stealth games for the computer, such as Dishonored or Assassin's Creed, we can take some tips and add them to our campaigns.
Objectives
This is the biggest change that a DM has to foster in his campaign. As mentioned before, the objective of stealth is almost always just to get in some extra sneak attack damage. Stealth gets boring when, in the end, it's only about combat. There is nothing wrong with sneak attacks, of course. Some of the most memorable moments in my campaigns have been sneak attacks (double crit + 4x backstab damage FTW?), but stealth needs variety.
The purpose of stealth is to remain undetected. Let stealth be a tool for defeating encounters. If the players successfully sneak around an entire group of hobgoblins, give them full XP as if they had beaten the fight. And don't just stop there. If you want great stealth encounters, turn it into a real challenge like Dishonored does. Make enemies move around somewhat unpredictably. Have your players use distractions, or find opportunities to pick off the enemy one at a time. Give them bonus XP or a better reputation for being able to complete encounters without bloodshed, similar to Dishonored. Also like Dishonored, make a few combat encounters really dangerous if you rush right into them, and be sure to make that fairly clear through in-game information.
Environment
The world is bigger than a grid. Description helps. Open up the terrain for movement, like Assassin's Creed. Let them sneak past the royal guard by balancing across the rafters of the great hall or by sneaking over the rooftops to bypass the thugs waiting for them in the street. Think in 3D even though the grid is 2D.
Light is a huge factor for stealth in a lot of games, such as Amnesia: The Dark Descent. It ought to be very important in D&D as well, what with all the torches, lanterns, and magical lights often found in its environments. Have players make strategic use of light. One campaign, my players doused a torch while the guard was on the other side of the building so that when he came back, he couldn't see them sneaking inside. Unfortunately, the sudden lack of light alarmed him, which leads to another point:
The Chase Sequence
The way you describe the ninja character as cycling through backstab -> run -> hide -> backstab definitely confirms this as a bad pattern of stealth. One of the biggest flaws of the first Assassin's Creed game was how you could stab someone, run like heck, hide on a bench right around the corner, then go back and stab someone else. Rinse. Repeat. Worst of all, until they introduced notoriety in later games, it seemed like everyone forgot what you did.
Dishonored is a much better example of how to do detection and chase effectively. On the very first detection, the enemy is immediately alert and aware of the fact that you do not belong here. Hostility begins right away, and the chase is brutal. In a chase, NPCs do not let you get away unless you do something really daring. In the TV Show Burn Notice, the main character remarks during a narrative in a chase sequence that the only way to escape a chase is to do something that the people chasing you won't do -- like jumping off a roof.
And even if you get away, the NPCs should not just "forget" about you. They should be on high alert until you die or they are convinced that you have been driven off. Enemies on high alert for a stealth PC should not be easy to catch off-guard. In addition, they should not be splitting up alone if they are even reasonably intelligent.
Have NPCs adopt tactics like the PCs tend to act when encountering stealthy foes.
All Alone
"But I'm the only stealth character on the team!"
This is roughly the ninja player's position, I take it. I've been there. Fortunately, you don't have to be reliant on stab-and-run to be useful. A number of the former tips are intended for stealth-based encounters, but here's what a stealth PC has gotta do to have fun with stealth while your allies are kickin' down doors in the name of Tempus:
1: Wait for the encounter to get started. Be out of sight on the periphery.
2: Sneak up to a squishy target.
3: Stab.
4: ???
5: Profit.
An ultra-stealthy character is ideal for taking out priority targets. Then, using other skills, such as acrobatic-type skills, make a daring escape. Not just running away by pure movement points, but dodging between pillars, leaping onto ledges, or tumbling past enemies to rejoin your allies.
Stealth should get you into the fray. Speed and tricks should get you out.
First, this adds variety to your actions as a stealthy character.
Second, it should be hard to lose detection when enemies are tracking your movements so closely.
Beyond combat, a stealthy character can still be a great asset. Perhaps you can open a gate while the party is fighting. Maybe you can sneak into a camp and rescue a prisoner while the party is attacking from the opposite side. Generally, you should avoid going too lone wolf unless your party wants you to do so, because that's dangerous and slows down the game for others. Performing a stealth mission while the party fights a battle has been the best possible scenario in campaigns I have played. It keeps everyone busy, provides a distraction, and lets your group benefit from stealth simultaneously.
TL;DR version: Stealth should be more than dice rolls. It needs to interact with the environment and the intelligence of the NPCs involved. It should be rewarding, fast-paced, and require cleverness more than just sneakiness. When done right, it should give the party big advantages as a whole.
No, you shouldn't have to ask about everything.
One of the good practices of GMing is remembering that nothing exists until you narrate it into existence. Your GM should have told you everything that your character can immediately spot without difficulty. This is one of the most important aspects of player agency that you have the capacity to make an informed decision. Information should only be withheld when it's deliberately obscured (e.g. true intention of a traitorous NPC) or you character fails to notice something difficult to spot (e.g. you failed a Spot Hidden Door roll). If you are in tall wheat, you should be told so, because there is no way your character missed it. The reason why he didn't establish that (pretty major) circumstance is either because he forgot, he does not understand that premise or that he wanted to railroad you into doing what you did.
Give GM some feedback
And ask him why he didn't tell you straight away that you're in wheat and say that you would act differently if he did. Say that you have nothing against ending the session with a dramatic scene, but you feel that this is not how you would choose to act, given whole view of the situation. Try to be polite and casual about the thing - he might get offended or upset, which is the opposite of what you want to achieve. If he does, say that you wanted to make sure you understand his intentions correctly.
Continue as normal
This might have been just a one-time slip. Don't worry too much, unless it happens again. If it does, then you have to talk to your GM with other players about your social contract. You might learn that in fact the game you're playing is more of a competition between the GM and the players, and you need to be on lookout - which is fine, but might not be what you want to play. In the end, you vote with your feet and if you fail to reach consensus, you can always walk away.
Best Answer
First of all, you need to introduce this topic to your GM by letting them know that unfortunately you're not having fun in their game, and this is a problem you'd like to reach a solution for somehow. Help them see your perspective. There's lots of great advice for this part in other answers.
I wonder if there's some kind of disconnect about the details of how you're asking to stealth, like if your GM wants you to describe in more detail how you go about it or what you use for cover. They're right that you can't just "go stealth" in the middle of an open room when people are already looking at you.
Stealth can be a matter of who you're hiding from; it's not always "everyone" if you're using cover that hides you from one side but not the other. (But "being stealthed" is a useful simplification, and moving from shadow to shadow along the edges of a street is the typical assumption if you don't go into detail. Or moving in a way that is unlikely to reveal your presence to people in at least the direction you're going.)
That sounds problematic.
Being too annoyed to even ask if you could stealth may be partially hiding the problem from the rest of the group and/or the GM.
In your first talk with the GM, you could ask after the fact if stealth would have been an option for you in any of the cases where your group got jumped. And if so, how/when you could have asked "properly" to go stealth.
After communicating how this is stopping you from having fun, maybe part of the solution could be having the GM let you know when the terrain presents any opportunity to be stealthy. (At least in the short term while it's a sore subject and you don't want to keep asking and getting rejected).
It would be unusual (and could get meta-gamey) for the GM to remind you every time stealth is an option long-term, but it might help you get on the same page with each other about the game world in the short term. (And heal your psychological wounds / rebuild trust with the GM about treating your character fairly).
In-world, your character should be able to recognize opportunities for stealth when they occur in the game-world envisioned by the GM. So having the GM tell you about the game world in the those terms does fit playing a character who focuses on stealth.