certainly not in a factory stereo.Regarding your FLAC files, if you convert them using LAME and V0 quality I guarantee you wont be able to tell
That being said, the OP might want to look into a device that he can put the rockbox open source software on. That will allow flac playback and should work fine through either usb or aux.
here's the wiki if you need more info/compatible devices
Rockbox - Wikipedia, the free encyclopedia