I have a pre and it really is just an option that is easily turned off on the location services card. It isn't hidden or devious. When you don't have it on, applications like Google Maps and the Navigation service ask you, as they are loading, whether you want to turn on the location services so they can work. I am more concerned about why they want to know what programs I am using and how often I use them.
Certain programs, like My Tether, allow you to tether your Pre to your laptop. It requires rooting your pre and installing certain services to the phone. Technically, I believe it is against Sprint's TOS. I have had to use it on occasion while traveling because I needed access to flash sites that aren't accessibly on mobile phones. If this application tracking is ever used as a reason to cancel my contract I wouldn't be to happy.