Most people don't take plea deals because they are too broke to defend themselves, by going to court you risk a much higher penalty if you lose. Would you take a guaranteed 12 months in prison or gamble on a 50% chance of 10 years?
EDIT: Why not make it a law that when you are found innocent then prosecutor's office should refund whatever it cost you to hire your lawyer?
The question, though, was whether a person in a criminal case would be reimbursed the cost of their defense by the government after being found not guilty.
Even worse is when the evidence is poor but they want to convict the guy anyway because he looks like a bad guy. "Even if he didn't do this, I know in my heart that he's guilty of other crimes."