Why does coffee seem to taste better in a ceramic mug than in a paper cup?

Couple of simple things:
Your perceived experience of drinking from a ceramic cup may very well be more positive than paper. It "feels" like a better experience because of all sorts of associations with your chosen cup.
A mug or coffee cup has different meaning from paper:
It's something you get at a restaurant or in your own favourite place to drink it (kitchen, living room, sofa...)
A paper cup feels temporary, and is more of a take-away, disposable experience.
You might drink from paper more often when doing other things, like travelling, or working at your desk.
Oh, and paper has a flavour.
When you heat a ceramic cup with hot water, you'll probably notice that it smells somehow *clean*.

Hot, waxed paper smells of hot, waxy paper. This definitely affects your experience directly: your coffee will taste (through smell mostly) a bit papery.