98 jetta factory alarm problem

My girl has a '98 jetta and the battery went dead. I put a new battery in it and now the alarm won't let me start it. It has a key fob which doesn't seam to do anything. I've tried locking and unlocking the doors with the key but NO luck. The dealer asshole says I have to have the car towed in and reprogrammed. I can't believe I have to do that just on a battery change. Any help would be most appreciated. Thanks.

Does it crank, but not start?