I am installing ceramic tile in my bathroom, and am wondering if I need to raise the
Floor flange so it sits on top of the tile, or can it stay on top of the cement floor?

Let it stay where it is and add an extension ring available at Home Depot and Lowe's.

I am installing ceramic tile in my bathroom, and am wondering if I need to raise the
floor flange so it sits on top of the tile, or can it stay on top of the cement floor?

As Harold suggested leave the flange where it is and purchase a set of flange extenders, (see image) good luck, Tom