When I do that exclusion tool in my scenery.cfg file, it removes everything including my airport. I only want trees and houses removed.

That's how an exclude works, it will exclude all scenery objects in a certain area. If you only want so to go, you must make sure that the reference points of the objects you want to stay are outside of your exclude area.

What happens if there are trees on my taxiway? There isnt any tool that will get rid of them?

If you have trees on your taxiway they are probably autogen trees. In that case it is much easier to place a VTP grass polygon around your airport (just like the default scenery has), this will remove the autogen objects, no need to make an exclude in that case.

thanks