I do have something I want to say about this. I really feel most people don't use/preserve their caps properly. By that, I mean you see too few caps on a map because people don't want to risk the investment in them, and then they're surprised that their lone or two caps are the first thing the enemy goes after.
That's not a shot at anyone, more how I percieve the issue.
I really feel there's a good rule for keeping caps alive and useful in ur fleets. Always have (# lvls of taxation researched - 1) lvls of cap ships slots teched. By that I mean, if you have three levels of taxation reserached, then you should have 2 levels of cap slots reserached and so on.
This keeps the best ratio of caps to fleet, because you must remember, capital ships are the best support weapons you have in this game.
It's tough, because the fact is caps are the most logical targets. They hurt the most to lose. The "healer" support caps help dramatically, but microing to keep an eye on your caps is a must. Don't let your cap get entangled in the fray. Keep it to the side. Close enough to do damage, but far enough that it can actually move if it needs to. One of the biggest frustrations is when a cap gets stuck and tries to change direction = death sentance.
My point is this. If you're only going to keep 1-2 caps once your fleets hit 300+ ship slots in size, you make your enemie's first target of choice pretty easy.
One of the few perks of rush maps seems to be that fleets stay relatively smaller so "cap targeting" doesn't have as big a payoff, so I'm assuming you mean in bigger games that last longer.
Good rule of thumb: Buy a second cap once you have your opponent on the run. ONce you are ready to start seiging your opponent's planets, get a second cap. It does wonders.
Guess my thoughts are gettin a little random here, but I think they all vibe together. Hopefully something I said here helps.