As gbaikie already pointed out, NASA is basically refuting the NYTimes story. It just sounds like NASA and the film production company didn't have a working agreement, so the agency isn't going to promote the film. Similar arrangements happen with the Department of Defense (DoD) all the time. A production company can submit their script to the military and, if the material isn't overly objectionable, DoD will often cooperate with the movie. Consider a movie like the 1980s "Top Gun". There was no way that movie could've been made at the time* without access to aircraft carriers and planes like the F-14. On the other hand, a movie that tries to portray soldiers as a bunch of homocidal maniacs, say "Platoon", probably wouldn't get DoD cooperation. That isn't any more unreasonable than expecting the NAACP to cooperate with a movie favorable to the KKK.

As for your basic question, at least some scientists do try to refute bad science. One good example is the Bad Astronomy website. It does not only talk about real astronomy, it does things like offer movie reviews from an astronomical perspective. Another one is Skeptic.com. There are probably many more such sites out on the Net that I don't know about.

Why don't more scientists speak out when bad science is shown in movies, TV shows, etc? I suspect it's because no one asks them (by that, I mean the Press) and too many people have a weak understanding of science. Today, science has become so specialized and the language of science has become so arcane that most people don't understand it.

Your post asks some good questions. Is climate change happening? Without a doubt - the climate is always changing and has done so throughout geologic time. Is the current change due to human activity? That's the real question right now, and there is reasoned debate on both sides of the issue.

As for a major earthquake going to hit California soon? Without a doubt, but I guess it depends on how you define "soon." It literally could happen at any time from now through the next few centuries. In geologic time, a few centuries is but a heartbeat. We tend to look at everything from the perspective of a human lifetime, so when we see something like the eruption of Mount St. Helens, the destruction seems so permanent. However, scientists studying the terrain have noted remarkable biologic activity in the area in the 23 years since the eruption. It won't look like it did before the eruption anytime soon, if ever, but nature is working to restore the area quite well.

*With today's CGI technology, it might be possible to make a movie like "Top Gun" now using computer special effects. That wasn't the case in 1986 when the technology was much more primitive and the computers much less powerful. 1984's The Last Starfighter pretty well shows what the state of the art was back then. I read that it took a full second of CPU time on a Cray supercomputer to generate each frame of video (and there are some 24 frames per second in a movie.) Today, a network of animation workstations like at ILM are much more powerful and sophisticated. More recent movies like "Sum of All Fears" show that you can create a realistic aircraft carrier on a computer, and "Behind Enemy Lines" did a good job of creating digital F-18 Super Hornets.