I'm trying to install a ceiling fan. I have four wire in the ceiling. Red,Black,white and ground wire. On the ceiling fan I have three wires, Black, White, and Ground wire. The instruction for fan states: Black to Black, White to White and Ground to Ground, which I have done. My question is what do I do with the "Red wire"?

The red wire and blackwire may be from 2 separate switches and you may not need 1 switch and 1 wire.
Verify what wire is switched with which switch, use that wire and cap the unused wire.