How did a thief start my car!?

Could have been towed. If it was joyrided though, it tends to indicate the thieves had access to keys. If it was recovered at a shop or parked somewhere, it might have been illegally towed with the intent of being stripped for parts. What does the police report indicate in that regard?

I don't think it was towed, because they broke on of the windows. I have not been able to actually see the police report because my name is not on the title, so I'm not positive what all they have in there. It was gone for 2 weeks though, so who knows if they made changes to it in that time as far as switching out the ignition or anything.

You can't just switch out an ignition module and drive away, you would have to replace or reprogram other modules as well, not likely to happen on the street or in a parking lot. The idea of 'stripping a column' for car theft pre-dates the current era of antitheft systems (just like 'hot-wiring'). They either had a key or towed it. Again this is all speculation without details from the police report.