I don't think there's that many people applying with stats that are that low. I definitely don't think its 50%. Remember, even all the people with 3.5's and 30's aren't getting interviews at every school they apply to. For an average of 15-20 applications, even well qualified people pull between 5-6 interviews. The numbers get spread around like that. Somewhat random actually, sometimes its just based on the numbers, sometimes its based on something they see in the app, some potential or something. The AMCAS site actually has a breakdown of stats for applicants and matriculants:
http://www.aamc.org/data/facts/start.htm
Remember, if you have stats that should get you in somewhere, doesn't mean you'll get an interview everywhere. But basically, the 3.5, 30 is just a general guideline that you're likely to get in somewhere provided that you have good ECs, LORs and that you apply to a diverse array of schools.
As far as letting you apply, most schools will send you the secondary no matter what. Its $$$ in the bag for them. It doesn't necessarily mean that you have a chance or that they'll even review it if you don't meet certain pre-screen cut-offs or requirements. However, there are several schools which will reject you pre-secondary if they deem that you're not competitive.
Anyways, hope this helps. Good luck.