1) Physics is not a very controversial subject any longer. The pope bent over and took it in the ass a looooong time ago.
2) Maybe he is a great teacher and has understood to keep his personal convictions separate from actually doing his job.
3) When Newton was alive the evolution of science was at a radically different place. It was way before Shopenhaur, Nietzsche and Thomas Khun. In the age of Newton a supernatural god was still the scientifically best way to explain the nature of the world. Science evolves.
4) Maybe it's not true. It sounds a bit strange that a guy with those kinds of beliefs could be hired to a position like that. Being a fundamentalist of any sort should discount him from any kind of scholarly position anywhere. I'm guessing the journalist had a go at creativity.