Just because the ship followed him to one event/location, doesn't mean it needs to follow him to every. Their thinking probably is "We can get good protection at this location through USS whatever, let's do it."

It might also be based on very practical things. The prez/vice always have a quick exit plan. The stockdale has a pair of helos that could have picked him up from anywhere in the city. That might mean they didn't have to lay on as many ground assets.