IMO bombers should be able to cause heavy damage to BS or cruisers but not single-handedly...
Take a look at their size. And then think about the hypothetical costs for cap ships. No one would construct these flying fortresss, if your enemy could bring along one bomber and destroy such an expensive construct.
I think bombers should be able to damage them (unlike normal fighters, which should normaly only scratch the hull a bit). The overusage of capital ships is another thing.
Capital ships are way to weak, but we can't buff them a lot since everybody would only fly caps then...
It's a dilemma. Our real problem is that everybody wants to fly one...