I think there's two reasons... When you're building up a romantic fantasy of the most incredible, intimate sexual experience, you're probably not thinking about using a condom. Since movies aren't real, they're free to just reenact fantasy, rather than mimic reality.
As I think about it, it's the romantic scenes, or at least the scenes where the experience is portrayed in a very positive light, where condoms aren't used. I believe condoms are used in both Superbad and 40 Days and 40 Days Nights. 40 Days and 40 Nights is particularly informative: as I recall, the main character uses a condom in a meaningless and ultimately unfulfilling encounter early in the movie, but isn't shown using one in the romantic scene at the end.
Another reason (or the response you might hear from a director) might be that they don't show the characters NOT using a condom, so they are simply avoiding focusing on the more prosaic aspects of the encounter.