I wouldn't worry about the top tube hitting your tender bits.... generally if you come off the seat and stand over, the bike will be tilted slightly one way or the other and completely misses them. More important is how the bike feels while you are riding it. If you aren't either stretched out too much and (more likely...) you aren't too cramped, I wouldn't worry about it.

Here's an article on bike fit by Sheldon Brown and an another from Rivendell which is even more to my point.