I'm not sure of the exact context, but the phrase itself originates from the fast food business. If you go into McDonald's and order a hamburger, you may be asked, "Do you want some fries with that?" It's become very much of a stereotype.
I've often heard this phrase used as a kind of taunt. If somebody is, for example, boasting about their wonderful philosophy degree, another person might say something like this:
"Well, we all know what happens to philosophy students. Start getting into practice now: 'Do you want fries with that?'"
The implication is that the student's wonderful philosophy degree won't help them get a good job. Instead, they will find themselves working in a fast-food restaurant, a job which is unpleasant, demanding but not intellectually exciting, and not very well paid.
That's one possible way of using the phrase. Can you remember what context you've heard it in?