I find that it is very common for some people (typically English teachers, in my experience) to use a comma before a phrase beginning with "rather than" when it falls at the end of a sentence. For example:
We decided to go to the grocery store, rather than a restaurant.
In the above sentence, the comma seems to be unnatural and incorrect. I can only think that perhaps they were taught to always use a comma before "rather than" when it is used in an appositive phrase, as such:
We decided that, rather than going out to a restaurant, we would go to the grocery store.
This usage is correct, and I have no problem with it. I think that people use the comma in the first example because they are incorrectly applying a rule that should only apply to parenthetical phrases. They might decide that the last part of the sentence is a parenthetical phrase because it is nonessential information, but if you replaced the words "rather than" with "instead of," few people would put a comma there. It just doesn't flow properly.
However, the incidence of English teachers perpetuating the first example is so great that I have to wonder if I have missed a lesson somewhere. Have I been incorrectly removing the comma all these years?