They were published by DC, but The Fountain is not based on any comic (the comic is based on the original screenplay), Stardust was originally published by another company (Vertigo only published an illustrated edition - I don't think there's even a comic).
And History may have been originally published by someone else also? It's creator owned anyway. Road to Perdition also fits in to this category.
So, no, I wouldn't say any of these are really DC/Vertigo movies, any more than any other adaptation of a book is a movie from that book's publisher, or any movie that has a comic adaptation is from that publisher.
Marvel did 2001: A Space Odyssey, Star Wars and James Bond comics, for example, and they're not Marvel movies.