Just to clarify, the OP seems to be asking four questions:
1) Is unflavored coffee, purchased from a treif establishment kosher?
2) Is it Ma’aras Ayin to enter a McDonald’s at a rest stop?
3) Any McDonald’s?
4) From a McDonald’s cup?
What strikes me about the cup business, is even if one should not buy a coke (or fill up water in their coffee cup) in their establishment b/c of Ma’aras Ayin (a point I’m not conceding), to not use the cup would be Ma’aras Ayin on Ma’aras Ayin. Isn’t that way too crazy?