Donald's characterization in this movie. Cowardice has never been his biggest flaw, or even a huge part of his personality. Not that he hasn't shown cowardice, but no more than any of the other characters. His major traita has always been his temper, and it only is really displayed in one scene in this movie (when Troubadour sings his You Suck song). It's not like it couldn't work as a believable flaw (it had been working for over half a century till that point), Pete could say he's too much of a loose cannon, that he flies off the handle at any slight (except, you kno, the way Pete would say), and that Muskateers need disipline.
Maybe they thought that a constantly angry character wouldn't be fun to watch. Or that he would be a too good fighter by always charging in...
Actually, this is a bit of Fridge Brilliance: Donald being a coward is an established part of his character; it's just that this particular trait is more a staple of the Donald who appears in comic books and strips than Donald in animation — and this movie is narrated from a comic book!
It varies from story to story just how cowardly he is, though a fair rule of thumb is that if there's another character with him who can play the brave hero (like Mickey or Uncle Scrooge) Donald is usually portrayed as a bit of a coward as a contrast; he's all gung-ho as long as there's no actual danger involved, but when things get scary he's just as likely to lose his nerve. For a good example of a "cowardly Donald," you can check out the classic Floyd Gottfredson comic, The House of Seven Haunts from 1936.