if she loves her crate, then use it... it is the safest place for them when in the car.
I also just posted in another thread for you... it could also be that she is getting motion sickness, try a something for that like a Dramamine (adult not childerns or the chewables)... do a half tablet. Or if you can get benedryl, that is 1 mg per pound.
Our girl HATED the car all her life no matter what we did or tried she just never took to it, we believe it ws due to her being out of control of what was happening... the movement of the car and she was not controlling it. Banks was very dominate and deliberate in her behavior, she never did anything unless she wanted to (with some protest when we did commands) so we had to have her somewhat sedated (prescription from vet) when we went on road trips with her.