A "kick in the pants" was an Earth idiomatic expression that referred to a startling incentive to forward motion or, more generally, an unwelcome surprise. The idiom suggests the effect of a literal kick to the butt, part of the Human anatomy covered by pants.
When discussing "first contact" with aliens with Lyneea and how she expected it to be so different, John Crichton agreed with her disappointment, saying, "Yeah, it's a real kick in the pants, ain't it?" ("I, E.T.")