In Rogue One: A Star Wars Story, the starfighters of Blue Squadron attacked on the Energy Conversion Laboratory on Eadu. They destroyed almost everything else but Director Krennic's Delta-class shuttle, even though it was a sitting duck. Why did they leave the ship unharmed?
The shuttle is, ultimately, just a shuttle. Krennic might favor that particular model, but it's not like the Empire is going to have any real difficulty finding another shuttle for him if something tragic happened to it. It certainly isn't worth risking pilots and ships by taking another pass over the facility.
In contrast, the research facility is a critical target. Erso and his staff, the equipment they were using, research data that might have been stored locally, all could be vital to destroying the Rebellion, and therefore were priorities for the attack force. With the ever-present threat of Imperial retaliation, their job was to get in, destroy the primary target, and get out if possible, not to engage everything with an Imperial logo on it. If targets of opportunity like a shuttle are hit, great; if not, no big deal.