This is based on a true event. Film pioneers August and Louis Lumiere made a 50-second film called "L'arrivée d'un train en gare de La Ciotat" (The Arrival of a Train at La Ciotat Station). It was first shown in 1896 and is, yes, just a 50-second shot of a train arriving in a station. The story surrounding its first showing is that people panicked and fled just as they did in the Civilization V intro. But did that really happen? Some doubt it really happened that way and is exaggerated. Confusing the issue is that in 1935, the Lumiere brothers shot a new video that was similar but used a 3-D film technique, so that the train did more closely have the effect of appearing to come out of the screen, and people also acted terrified and flinched. Together, these events have taken on a mythic quality connected with people's reactions to the early days of film.

What the truth is, I don't know. We've all seen people flinch at 3-D footage of things being thrown at the audience, even though the audience knows it's just a film. We've seen people get nauseated at film footage of a windy drive or frightened when film has simulated a person falling from a height. It's plausible that people watching perhaps their first film ever, in 1896, may have had a more extreme reaction to the footage than we would today. It's also plausible that people seeing a 3D film for the first time would instinctively flinch at the impression something was about to run them over at high speed, even though they knew it was just a movie. It's also quite believable that these reactions may have been exaggerated with each telling, by people talking about it and emphasizing the naivete of people of yore. Whichever it is, that Civ V intro was an homage to that incident.

By the way, you can watch the original footage for yourself on YouTube, just look up "L'arrivée d'un train en gare de La Ciotat".