Most scifi I've read with FTL usually has some explanation that isn't pure fantasy. For example, I just finished reading A Fire Upon the Deep[1] by Vernor Vinge, and the in-universe explanation for FTL in the novel is that different regions of our galaxy effectively have different laws of physics, which is (admittedly somewhat handwavingly) due to the density of the interstellar medium.
Sure, FTL travel is never grounded in our understanding of physics and the universe, but do you really think our understanding is anywhere near complete?