'Salem's Lot refers, most directly, to the setting of the novel—the town of Jerusalem's Lot in Maine (King's home state). That setting is, in a lot of ways, the protagonist: the book's about Jerusalem's Lot, first alive, then undead. So you could say that the novel's title is another way of saying either "small town" or "vampires"—or both (see "In a Nutshell").
The shortening of the name is probably meant to suggest the Salem witch trials, evoking general spookiness and devilry, even though the book doesn't have anything to do with witches or Salem. That's marketing for you—and even vampires need marketing (especially when they sell antiques like Barlow does). The novel was originally titled Second Coming (source), referring perhaps both to Ben Mears' return to Jerusalem's Lot and to the dead returning to life.