SF movies will always be popular, honestly, because the Fx are great and you can't get deep into the science without slowing the movie down too much. Movie goers are more willing to throw disbelief out the window than book readers are (probably because it's the difference of an hour or two for a movie and anywhere from an entire evening to a month--or more--devoted to reading a book). Because of the different handling of the genre in the two media, I think it's a vast disservice to compare the two to judge SF's popularity.
But, I also see this as just the cycle that interests go through. SF had a golden age, where it promised the best future, science would solve all the world's problems and offered the best stories and Fantasy, Horror and Mystery barely got published. Then Horror got very popular and rivaled SF but took a turn and almost died with very few books published for over a decade. Mystery has risen up in the last 15-20 years and is now starting to threaten Romance's dominance, with Fantasy coming up behind and SF dropped down to single digit percentages.
It all flexs because people glut on something for a few decades and then get sick of it and turn to something completely different.
Genres only die out if its authors aren't exploring it fully and reinvent it during the "lulls". Stephen King reinvented Horror. Anne Rice reinvented the vampire. Tolkien reinvented Fantasy (though it took him 20-25 years to become popular). SF is lulling right now. If you love the genre, follow your visions and maybe you'll be the one that reinvents it and brings it to the fore again.