I busted my ass at a startup for years and also lost the political game. So I'm speaking from experience here.
You can either get all mad and worked up and pissed off about it, and waste years of your career (as I did) being pissed off, stubborn, and refusing to change. Or figure out how to play. I'd like to think there are places with better politics but I think it's pretty endemic of large organizations. I'd love to be proven wrong.
The thing is, "working for yourself" is so flawed in so many ways. In the first place, nobody "works for themself". You might work for customers, or clients, or whatever, but not "yourself". Second, you're a lot better off working at a good company -- MUCH better off -- unless you have a pretty damn concrete idea of what you're doing. In addition to the income, the big company will provide better networking, more credibility for anything you do subsequently (whether a new job, fundraising, hiring--ANYTHING), it's an all-around better gig.
I'm just trying to save you a lot of wasted years and time here. Take it or leave it.