I am sure you'll get a few nibbles because of that GRE score. Hopefully you can get some schools to see that you really are academically talented despite your bad grades. I totally believe you that your classes were harder than many other people's due to the school you go to, however the unfortunate truth is that that is rarely taken into consideration in PT school admissions. What grades you get matter, where you get them doesn't. So having such a low GPAs, especially pre-req GPA, is going to kill your application at a lot of schools, that's just the sad truth. But there aren't a lot of applicants with such a lopsided application (ie 99th percentile GRE, but well below average pre-req GPA, cGPA). I honestly am not totally sure how that will play out. But I think if you apply and interview strategically you will end up with at least one acceptance.
Also realize that interview scores and variety and breadth of experience in observation hours both play a huge a huge role too. LORs and essay also have an impact to a slightly lesser extent. These are all areas where you can do yourself plenty of favors if you are diligent.
Hopefully there are a couple of other low GPA, high GRE people that can chime in. Also I strongly recommend taking time to study the ACCEPTANCES, ETC sticky at the top of the forum. You can get a good idea of what kind of stats have gotten people into various schools. You will also learn that this process is incredibly random and stochastic and it is very hard to truly prognosticate what someone's chances are.