Last year I applied to 9 schools, got rejected from 8 (one post-interview) and waitlisted at what I thought was my safety. It sucks. I doubt there is really anything anyone can tell you that will make it suck less. But I'd be willing to bet money that you are "good enough". The fact that you took the time to apply in the first place, and convinced 2 or 3 academics to write you a recommendation implies that you are. The whole process is just kind of random. If this is really what you want to do, please apply again!
Btw, after sulking for a month or so I got my shit together and started looking for post-bacc research positions. Now it looks like I'm going to be doing a PhD at the university where I currently work, and I couldn't be happier.