It doesn't do extra damage like other moves. The main downside to this is that most pokemon that learn fly are flying types, so they are likely resistant anyway.
Hang on let me test this. Stand by for edited answer. this couldtake awhile, I have to go through have the elite 4 in my ruby. 1st person down. 2nd person down. thx, groudon and Blaziken 3rd person down.
Finally, Its still the same as if they hadnt used fly, not very effective to flying types.
Same as it would be normally, I think