Ben,
Carl's right...the choice of primer color is influenced by 2 factors mainly. The first is what you're using the primer for and the second is the colors that will go on after the primer. I work with kits that are molded in light gray plastic usually so the darker color helps ensure I don't have any bare plastic surfaces and it also happens to be a durable paint that's excellent over metal parts, so I kill two birds with one stone there.
Others will use the primer coat to "pre-shade" for monotone schemes, so they will lay down a light colored primer, then apply a dark 'pre-shade' color such as black or dark brown or even dark green depending, and they use the lighter primer color to contast with the pre-shade lines when they apply the base coat color over it.
As with many things in the hobby, it all boils down to what you're aiming for and there's no one magic single answer for the 'why' things are done. HTH!