Fengshui is natural and if done correctly you will feel very comfortable. For example, you don't have to engage a FSM to tell you that sitting at a desk in a room with the door behind you will make you feel uncomfortable. You can't see the person when he/she comes in!
My FSM Master Zhang told me before that he has Christians (Chinese & Caucasians), and Indians (Hindu) among his customers.
So in my opinion, fengshui is about seeking balance with nature and nothing to do with religion. In fact, the Tong Shu was charted by Muslims in the Imperial Court (I can't remember which dynasty though)