Bavaria, slowly but surely, is changing.  Due to its relatively booming economy, people from other parts of Germany are moving in.  Sort of like the Southwest US.

Or maybe Bavarians themselves are doing a bit of the changing, too.  Young Bavarians are far more secular than their parents and grandparents.  

Here's what I've seen in a small Central Bavarian town, between Regensburg and Nuremberg:

Elderly Bavarians - very Catholic; my little town's church bells ring repeatedly at 6am (to wake all decent people up) and again at 7:15am (because morning Mass is at 7:30am).  Both of these times are very important for old Bavarians.  Several of my landlady's Gasthaus patrons, when asked who they wanted for chancellor, said Stoiber (very conservative head of the CSU).

Middle-aged Bavarians - still pretty Catholic; generally make it to Sunday Mass, quite scandalized when someone gets a divorce (but somewhat less scandalized by someone having a child out of wedlock).  Mixed on the election, with a surprising number who were fans of Schroeder, if not his party.

Young Bavarians - living with their significant others (marriage is for people over 30) and popping birth control pills with even more eagerness than their American agemates (with good results) and making it in for church on Christmas and Easter, mostly for family reasons.  Apathetic towards election, many considering voting Linkspartei as a protest.