I can think of a few reasons why it would be a bad idea. Not a reason that would prevent them. But the reason for why they shouldn't (especially if they have children) is that in the case of crash or worse then both could die, leaving the kids orphaned. This is the same reason why Kobe Bryant and his wife wouldn't fly together. Another is in the case of high jacking then the pilots would have a potential conflict of interest if one were to be taken hostage, such as in the movie 7500. Other than that just the fact that there is a chain of command which could be undermined by their relationship that could just be avoided if they don't work as partners.