I suppose I don't like spreading myself out. Either my attention, my payment information or my loyalty. I started with Kickstarter, I think it's the better crowdfunding site (for US/UK at any rate ><) and it's where the majority of big and/or successful projects are happening.
Plus some of the ways IndieGoGo allows you to fund projects isn't something I'm comfortable with. Projects like the one where the guys wanted to buy the rights to Homeworld, and using some open-ended funding method for it, just sounded like bad business to me. There's plenty of bad business done on Kickstarter as well, but due to their exposure they tread a little more carefully.
Mostly though, IndieGoGo is the underdog, and these projects live or die based on the volume of eyeballs and wallets they get exposed to. Like Pnx said, these projects have to build inertia to generate funding, and Kickstarter is far better at that than IndieGoGo. Even if there's a project I like, I rarely back unless I feel confident it's going to make its funding goal. Why? I dunno. I don't like pledging cash to stuff not knowing whether or not it will succeed. The fact my transaction is only processed if the project is successful doesn't matter. I don't pledge for $200 worth of stuff expecting only $100 of it to actually succeed...I pledge x knowing that it's going to cost me x and there's no guesswork involved. Put another way...I don't like having potentially random amounts of cash withdrawn from my bank account every month. I like knowing exactly how much I'm going to spend on a number of successful projects.
I admit it's a totally irrational position given the way these things work, and yet it's how I roll with crowdfunding projects.
So yeah. There's some paranoia, some irrational behavior and the reality of how crowd funding works best, that guides which site I choose to give my money to.