I never used any of these protectors for my 3G but a buddy got it for his Pre and it had bubbles in the beginning as well. I think it needs a few hours/couple days to become bubble free.
I got mine now for a year, dropped it several times and the screen is pretty much prestine (no case either).
It has scratches on the back though.
Wife dropped hers once and has a scratch of an inch.
Good decision on the protection, give it a few more days.