My understanding is that Chrysler does not own the cars or the museum. Chrysler converted it to a non-profit or some other type of separate entity - I forget the formal name for it. This is actually what saved the museum and the cars as long as it did, otherwise they would have been sold off when the auto industry meltdown happened (was it 2008?). The problem is that the museum did not draw enough people to cover the bills. Likely it is tough to do at with the Ford Museum just around the corner. And yes, I am a true Mopar guy, but the Ford museum is awesome - it's no wonder the Chrysler museum suffered.
But I totally agree it is sad to see it go - it was really cool.