Everything goes according to plan, you establish a new market, lots of free customers get introduced to your product and love it and you skim off the cream that want power or enterprise features as your paying customers. What stops a new competitor from swooping in and saying they have something very similar, they aren't going to be spending anything supporting free customers, and with presumably lower costs, charging their customers less? With complete focus on paying customers, they might provide a better product too.
I don't argue with you that freemium works in the short and probably medium term, and it's great advertising. You have a great service going, and I think in your case, you build a lot of good will among developers hosting public code for free. But in the long run, in the general case, and assuming no network effects, I think there's a way to undercut such business models by focusing 100% on the paying customers.