We are considering staying in Prague w/ a new car but have heard car theft has been a problem in Prague. Any recent experiences or suggestions on this topic would be appreciated.

I thinking driving a new vehicle in Prague might be more of a threat than parking it. ;-)

Where will you be staying/parking? That makes a big difference!

Definitely be concerned. I would not drive into Czech Rep. with a new BMW. Make sure you have a guarded parking (garage is best). My Czech friends from Prague tell me horrible stories about car theft.

I think the key here is location...
Obviously, a dark street in Zizkov is riskier than a side street right off Wenceslas Square that has cops standing on the corner. If you are staying in a hotel, see what the situation is. Some places have gated lots in the courtyard behind or between their buildings. That would be ideal. Yes, there are many car thefts, but tons of people drive cars there, so there must be a way...!

When I was there last year there were a lot of cars with those wheel locks on them. That was the first place I actually saw those, so that tells me you might have a problem.

"a lot of cars with those wheel locks on them"
Can you describe the wheel locks?