I dismantled an old shower on a concrete slab. I plan to tile the bathroom floor. What do I use to cover the floor drain before I tile the bathroom? Can I just pour mortar down the hole?

I'd stuff an oil soaked rag down into the hole about 2" below the new surface, then butter on top of the rag with thinset to smooth out the surface. I am assuming you are totally eliminating the shower all to gether

Yes I am eliminating the shower in the guest bathroom to make room for a cabinet. Never used the shower. I have removed the tilefrom the shower and the rest of the floor. The hole will be covered by the tile. What is the purpose of the oil soaked rag?

It will better seal out sewer gas than just a thinset patch which will/may crack over time.