Piskei Teshuvos 135:25 says not to transport it past a dirty place even if covered. Seemingly, it should be forbidden to drive past a beis hatuma (church) with a sefer Torah. Or is it allowed?
It is permitted. The source of the Pischei Teshuvos is the Bais Shomo (O:CH end of siman 34) that when transporting a sefer torah outside one should be careful not to go near tzoah or other dirty things. This is since it isn’t kavod for the sefer torah to be in an unclean place, and a place that we are not allowed to learn torah or even think torah thoughts. The reason we don’t walk near a church to distance ourselves from the house of an Avodah Zara, but that is only not to be within 4 amos. Which would not apply to the street that the car is driving on, which is more than 4 amos away.