This previous thread answers the question pretty well.

http://www.reddit.com/r/AskHistorians/comments/zv7o3/why_did_ancient_rome_feel_so_threatened_by/

The Romans were tolerant of different religions in the empire as long as they accepted the divinity of the emperor. Christianity, being monotheistic, obviously had a problem with this. Judaism got a pass because it was a long-standing religion and wasn't really big on proselytizing. Christianity, on the other hand, was basically a new-fangled cult which was big on converting others. This essentially amounted to sedition against the empire.