That was only in the first couple episodes though, right? It seems like the writers nipped that problem in the bud early on. And yeah, Voyager sounds better than The Voyager, perhaps because The and the syllable "Voy" just don't flow well together.
*MY* pet peeve though was that trend was carried over into Enterprise. I realize that in the modern Navy/NASA tradition it's the unspoken rule that there's no "the" before the ship's name, but it just didn't sound right for the rest of Starfleet, nevermind Enterprise -- saying "The Enterprise" is an unspoken rule in Star Trek, particularly in TOS, TNG, and the films, but even whenever DS9 and VOY writers outright referenced the ship. Though, thanks to Netflix I've noticed that TNG occasionally called the ship Enterprise, without "The".