You must turn off the radio before disconnecting the battery or applying a jump-start, to protect the logic circuits. You did not, so now you must replace the radio.
--supplement from Kadanis --
Based on this post I thought my radio was dead after disconnecting the battery. The radio did not even come on in safe mode. However, I pulled it out (using nail files instead of the official removal hooks) and found that the 10 v fuse at the back of the radio needed to be replace. Once done, it came right back on and I had no problem.
One note, however, it is very hard to put the radio back in. The cables have to be pushed way back down behind the consol in order to create enough room to push the radio in the last 1/2 inch. I couldn't do it myself and had to get someone with one of those long grabbing gadgets to reach in from behind and pull the cables down. It was tough. Maybe someone with more experience can suggest a better solution for that problem.
dear fellow vw owners if you have a problem with your radio safe mode function and not sure how to ( example 2000 beetle )program your radio please follow this advise (decoding the radio)
The radio should be decoded when the vehicle is taken into the workshop and it has to be decoded if you sell your vehicle.
Continue to hold the AM/FM BAND and SCAN BUTTONS until the display changes to 1000 and then goes blank.
SCAN BUTTON until the word "Code" is displayed. After releasing the buttons, the radio statin frequency is displayed. The code has now been erased and the radio is no longer theft protected. any further help you can go to this site http://www.nwlink.com/~vdb/vw/Electrical/Coding_Radios just copy and paste into address bar im a mechanic myself and any help is much appreciated