Now, perhaps the police are very good at their jobs and really do get the right guy 90+ of the time (everyone who pleads guilty plus everyone convicted at trial - approximately 60% of cases that go to trial [2]). Or, perhaps the court system has a bias towards finding people guilty.
One data point that argues for the latter possibility is that people defended by public defenders are significantly more likely to go to jail than people with a private lawyer. People with a public defender go to jail 88% of the time compared to ~75% for people with a private attorney [3]. To me, the implication is that the skill of your lawyer, and the time your lawyer will spend on your case, has a huge influence on your likelihood of getting convicted. That influence implies to me that the police probably aren't 96+% accurate in getting their man, and that therefore some of the people pleading guilty are doing so to avoid a false conviction.
If you look into this, you'll find prosecutors threaten defendants with harsh punishments as a tactic to get them to plead to vastly reduced sentences - e.g. "Take your chance at trial, kid, you'll do ten years for possession with intent to distribute. Or, plead guilty, do six months with two years probation." Prosecutors are incentivized to make these deals because they are evaluated, in part, by conviction rate.
1-http://www.uscourts.gov/about-federal-courts/types-cases/cri...
2 - http://www.justice.gov/usao/reading_room/reports/asr2012/12s... page 14