1. According to Gizmodo the door was broken in because the journalist wasn't at home. He was having dinner in a restaurant, arrived later when the search was already in progress. The authorities acted respectfully with his belongings, etc. There is a huge difference between ringing the bell a few times and breaking the door when nobody answers and driving a truck through the front door at 60MPH, just because you can. Jon suggests the latter approach was taken.
2. He said that Apple claimed the prototype wasn't theirs, and that they didn't want it back. Comedy Central completely made this up! Apple definitely wanted the device back the moment it got lost.
3. Stop hammering on the "THEY BROKE THE DOOR!" bit. It's completely standard police practice, and it's not the Wrath Of Jobs.
That said, it goes without saying that Apple isn't the little guy anymore, and calling out Apple for its Big Brother tendencies is completely fair.