Welcome to the forums! And thanks for your support, glad you're enjoying the game.
The fighter/bomber cruiser balance is the way it is for a number of important reasons. Basically, the cruisers are big and slow artillery, which as you know tend to generally be weak to small, faster "common" units (footsoldiers, fighters, whatever). Fighters, by the same token, are built to be up close and personal to those sorts of giant ships, and thus don't take a lot of damage from them.
The bombers are heavily shielded, which is the main disconnect from many other RTS games -- that is vital for the functions of the bomber, such as for extended sieges of force fields and other similar heavy structures. The way that shields in this game works, range of the attacking ship plays a big part
. So cruisers, because of their high range, become the natural enemy of shielded bombers.
Bombers, by the same token, have an attack that does a huge amount of damage, and fighters have relatively lower hull strength. So it's entirely logical also that they would be weak to bombers, and they are all but useless against bombers in return because the low range of fighters makes them unable to effectively penetrate the shields of said bombers.
All of this came about from a logical analysis of the gameplay mechanics in this specific game, and the niches that all of the ships needed to fill. It would be extremely game-breaking to change it, though I understand that it is inconsistent with other RTS titles. That inconsistency was not casually done, and given the shield mechanics I can't think of a more sensible way to handle it.
But thanks for checking! It's good to do a sanity check every so often. I'll put this up on the wiki, because this has come up before and I don't remember where the other answer was posted (but it was essentially the same as this).