I don't think it's true of all films or all video games for that matter. Certainly the bad or misguided scientist is a Hollywood trope since the WW2 era, but a lot of the time I think its just down to truly dire script writing rather than an agenda.

For example, Star Trek Voyager (ostensibly a pro-science series) produced some horribly anti-science episodes, almost certainly because the script writer (and possibly director) was scientifically illiterate.

But there are exceptions: I thought that the scientists in Cameron's otherwise cringe-worthy Avatar were sympathetically depicted. In Fallout 3 (videogame) there are good scientists such as the "Dad" character as well as scientists who have ended up on the wrong side.

On the other hand, religious characters (priests etc) are frequently depicted as bad, evil, insane or manipulative as well.

I think that lazy writers like to use stereotypes that they reckon the audience won't have any trouble understanding. It's not so much an agenda as sheer creative laziness.