It *kinda* made sense for me.  Granted, I didn't see it working out, but them ending up together in the first place made complete sense.  Through the fourth book, neither of them really acknowledged her as a girl.  Naturally, this bothered her, and she made that clear.  Harry started waking up first, but he ended up chasing Cho and then having the on and off again with Ginny.  Ron is actually the first of the two to have acknowledged Hermione at all, shortly before the three set out together.  This had to have meant a lot to Hermione, because throughout the books she consistently had a low self esteem.  As simple as Ron's gesture was, it was a lot to her, and I think she went for him just because he made her feel more special.  Also, Ron is a little difficult at times.  Harry is generally mature and somewhat thoughtful, whereas Ron is frequently chided for being an insensitive prick.  Because of that, genuine thoughtfulness from Ron would mean more to her than it would from Harry, and mistakes from Ron would be forgiven more easily than Harry's.  Granted, none of this makes for a healthy relationship, but it sounds like a ton of relationships I remember seeing when I was a teenager.