Securities are more closely regulated than commodities in the US. I'm not sure what the laws are in Japan, where Mt. Gox is located, but I expect they could find some legal pretense to raid the exchange. There may be more exchanges popping up all the time, but almost everyone uses Mt. Gox. As a result, they're holding a huge amount of bitcoins and digital cash. That makes it a major target for a raid.

I wonder if they will start keeping backup servers in multiple countries, like Wikileaks? I'm not sure if that would protect peoples' digital cash, but their bitcoins would be safe in the event of a raid on the main server.