First, in order to get a clearance you have to be sponsored. Companies have a limited number of sponsorship slots allocated to them by the government.
Then, the process behind getting cleared is fairly arduous. You may have a clean record but you have to prove it exhaustively even for the lowest level of clearance -- I believe the application form is on the order of 40 pages. You have to list all of your friends and sexual relations from the past 10 years, for instance, so that they can go an interview every single one of them.
Essentially, being born and raised in america and having a clean record while being sane is just a baseline requirement.