First thing first, at the time secularization happened, Teutonic order was a shadow of its former self, having lost most of its' lands, power and prestige in the preceding century. As for why it actually happened, well, it's actually a bit funny because the best theory I've heard is that the last Hochmeister (Albert, soon to be a duke of Prussia) actually, honestly converted to protestantism. This would make him iffy of being a head of something that's supposed to obey the Pope.

The second theory is that the financial situation of the Order was simply too bad after their most recent war with Poland, leaving Prussia devastated.

None the less, Albert transformed Prussia into a hereditary duchy for himself, so he made a tidy profit there, and was rid of the rather restrictive Teutonic Rule.