Then your team was horrible at targeting GS downs. Bombers and GS are pretty much dead weight againts a team of competent scouts. You know, the ones who dont fly in a straight line and actually aim for GS/Bombers first.
I would say the onyl way GS and Bombers can be effective is if you have multiple ships guarding them. Their slow mobility prevents them from acquiring the biggest advantage- power ups. And a scout in damage and engine power ups can deal some serious hurt.