I'm sure there's several factors: Stress on the rider, number of commitments, injuries, logistics and so on.
For example, Astana has a team riding in both the Vuelta and the Tour of Missouri (happening at roughly the same time). The team manager might see that there are certain riders more suited to one course than the other, so they go there. Or the Vuelta might be skipped by certain riders because you want them in the Worlds, as mentioned in an earlier thread. I'm sure the riders have some degree of pull, but a lot of time I'm sure it's not their decision in the end. Even Lance.