For your perusal superfleet: http://spreadsheets.google.com/pub?key=p7xc_snd9Cc-6o2UwvPEWUg&gid=1
Notice that anti-strikecraft class ships (i.e. Flak) do 150% base damage to fighters but only 75% to bombers. Notice also that fighters have the same to hit chance as flak for attacking bombers but do 200% base damage.
Flak frigates are the counter vs. fighters, but versus bombers they aren't actually that good. A strong fighter screen is the only thing that will protect you from bombers adequately.
If I take the Advent Defence ship as an example it has a DPS of 18 split 3 ways. So assume one gun at a time can fire at a single advent bomber squadron. It is doing (18/3)*.75*.75 DPS to that squadron =, or 3.375 DPS. Each bomber has 75hp so it takes 22.2s to kill a single bomber.
Bearing in mind that there are 7 bombers in a squadron, you can see that it's going to take a while.
Working out the numbers for fighters being flakked, it taked approx. 6.3s to kill a single advent fighter (9 per squadron).
My point is that fighters and special abilities are the only proper counter to bombers, fortunately, bombers are only good vs buildings, HC and caps.