Wow that sucks. Going through college living in the city (and a couple years in a very bad part of the city) my roomates and I were subject to multiple car break-ins but never any home break-ins or anything so serious. I hope you can get to the bottom of finding out the truth, and recover your stolen stuff one way or another.
Was the safe hidden, or easy for someone to find? If it were hidden well I would tend to agree that it was someone who knew you, and where it was.