The courts for the most part. Or at least that is the public perception.
The sentencing guidelines maintained by the courts have all sorts of criteria for reducing the sentence that can be compounded to skew the result heavily towards the low end of the legally mandated range, and many times even below the legal minimum. For example, people who were drunk when they committed crimes often get away with lower sentences because "they probably weren't aware of what they were doing." Bonus points if you have a wife and kids to feed, pay a token amount to your victims as compensation, get your mom to write a letter to the judge, and/or act like you're sorry on your day in court. Some of these criteria have good reasons, but allow them to be compounded and that's how you end up with "you're guilty of raping your coworker, but you may go home."
Is this because of the courts or prosecutors? I don't see the latter being lenient with a fugitive.