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 appositive phrases. They might decide that the last part of the sentence is an appositive 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?