By pleading "not guilty" the defendant opens him/herself to a long, drawn out trial by jury, where, if the case is decided against the defendant, the judge is mandated to hand down the maximum sentence. (For a goofy example, just take a look at New York State's horrendous Rockefeller drug laws: plead innocent (even if you're guilty as sin) you'll likely be out in under five years; and yet if you plead "not guilty" (and have no previous prior arrest, not even a parking ticket, and are definitely not involved in drug use) the judge is mandated to hand down punishment for a much longer sentence (something reaching between 12 and 25 years with little chance of parole, via the jury's opinion of deciding on the guilt of the defendant.

Sadly, even the most innocent will accept a plea bargain deal -- even if they might have some ability to pay for legal defence counsel -- but since most defendants rely on a court appointed lawyer, they fail to receive the adequate defense they need, and wind up taking the plea bargain even when they're completely innocent.