In general I agree - in late-game, GP are less useful and I usually trade them in immediately for a quick golden age. However, unless you have absolutely everything, great scientists and great engineers do have some value, and there are use-cases where the rest are useful as well, I've listed them below.

Remember golden ages are always great, even if they are short. +gold, +production and no happiness issues.

Great Scientist: if you already have everything then this is indeed useless, but as long as you don't this is still useful. It's true late-game technologies are usually researched quickly but there are a few wonders in late game and being the first to reach them can be nice; furthermore, being the first to unlock Aluminum or Uranium is good because you can plan your land acquisitions better.

Great Engineer: there are some wonders in the late game, and they are pretty good actually. Other than that, great engineers are useful if you create a new city in the late-game; I usually buy a lot of buildings whenever I do this, but a great engineer can save a lot of money by speeding the most expensive buildings.

Additionally, factories are always useful.

Great Merchant: whether you should use the diplomatic mission or the golden age is not always obvious - see my answer to another question to see my opinion. In general I say a diplomatic mission is usually worth more gold, but a golden age also nets production. Custom houses are not worth it, in my opinion.

Great General: I almost always trade them for a golden age immediately, with one exception - I sometimes build citadels in natural chokes or other appropriate locations. From experience, a single citadel in the right spot, backed by 2-4 units, can stop an army.

Great Artist: the most useful type in the late game! Using the culture bombs allows you to reach practically everywhere. I one time used 3 of them to get to just one Aluminum patch in the middle of an icy area (just took a little time because of the cooldown). They can also be used to steal stuff from civilizations and city-states.

Also, landmarks are always nice in cities that already have a lot of +% culture.

Regarding city states: I usually do use great people from city-states, late-game maintenance costs are high but I think a golden age is always worth more than the time it takes them to get to the nearest border, even if it's a golden age lasting just 3 turns.

EDIT as of the June 2011 patch, great person improvements have been buffed:

• Erecting a great person improvement automatically connects a strategic resource if there's one on the tile
• Each great person improvement has an associated technology which increases the tile yield when researched
• Completing the freedom tree doubles the tile yield

This means using great people for improvements is a more viable option now.

Expenses

The top two things that cost you money in Civ 5 are:

• Buildings
• Military

To reduce the first one, be strategic about what you build where. Cities should be focused on a task. Pick terrain, tile improvements, and buildings that compliment this focus. For instance, if you are building a production-focused city, build it near hills and forests, and focus on military and production enhancing buildings. Don't build science or cashflow generating buildings, since you won't be producing much of those in this city.

Likewise, if you are building a science focused city, don't build military or other production enhancing buildings there. The city's focus should be on science or economic enhancing buildings instead.

The only exception is happiness - in order to maintain a positive balance on the happiness scale, you'll likely have to build some happiness generation buildings in most or all of your cities. This tends to be one of the largest trade offs economically in most of my games - do I make the people happier, or do I bank some extra gold?

You can also guide each city's governor to focus on a particular area, and this can help your citizens understand what they need to do in order to support your vision for the city. If you leave the governor alone, the city may ignore some of your tile improvements in order to work tiles that create something you're not interested in, but which makes the city's output more balanced.

Also, don't let your workers run free - focus your tile improvements on whatever works best for the city the tile is in the radius of.  Automated workers don't always pick the best terrain improvement for you.  They may destroy forest or plant farms around a city that is going to be production focused, for instance.

Every unit you produce costs you money every turn as well. Try to focus your attention towards a small, but mobile army, and don't fight on multiple fronts if you can avoid it. Mixed unit tactics involving ranged artillery units and close-up front line fighters work best. The AI is terrible at war, and they will generally start on the offensive, even though you've likely got your army massed and ready to funnel them into a meat grinder.

If you find yourself with a strong surplus of units, gift some to an allied city-state. You'll gain influence with them, and if you declare war, those units are likely to still benefit you indirectly.

Income

You gain money via citizens assigned to money-generating tiles, trade agreements with other Civs, and by trade routes between cities. Any duplicate of a luxury resource does you no good - it is there to trade.

If you end up with 2 of a luxury, or more of a strategic resource than you need, find someone rich and sell it to them for a tidy profit. Suppling your possible enemies with strategic resources might sound like a bad idea, but since you control the flow of that resource, if they start doing something you don't like, you can cut them off and drastically reduce the effectiveness of any resource-requiring units they produced in the meantime.

There's also a glitch that I don't believe has been patched whereby if you destroy a luxury good improvement (thereby reducing the amount of that luxury good available) you can end a trade agreement early at no penalty, and then rebuild the improvement and sell the good back to that same Civ for another sum of money. This could be considered cheating, and I imagine someday it (will be/has been) patched however.

Roads between cities are generally profitable, but you want to try to minimize the number of redundant road links you have, as having 2 roads between 2 cities counts the same as having one, and costs you extra.