The obvious solution to those who want bomber aircraft on carriers in to create a new unit, the Strike Aircraft. It would be a fighter without the air superiority misson, and have roughly half the bombard damage of a modern bomber. If you wanted to get fancy, you give it a slight bonus against SAM infantry due to the jamming pods these crafty employ for defense.
But, as I have stated in other threads in the Gen Disscussion forum, the entire modern navy needs to be reworked in civ IV. Hell, navies have always been thin in civ games, but IV is taking the cake... so to speak.
I have proposed the following new units and changes to existing units:
*ASW choppers, Deployable from Pocket carriers (2 units) or Destroyers (1 unit) They detect subs on recon missions, and can attack them on strike missions
*Strike Aircraft (see above)
*Cruise/Anitship missile treated as an aircraft, ignores fortifcations but not culture defenses, interceptable
*Tactical Nuke same as Cruise missile, but has 75% chance to kill anything in target tile, leaves fallout in target tile only, 40% of the time
*AGEIS type cruiser/destroyer units for carrier air protection with a much higher intercept rate than the standard destroyer.
*Upping the carrier to 4 fighter & 4 strike aircraft.
*Nuke subs with 3 ICBMs, OR 3 cruise OR tactical nuke missiles.
*Essex/Pocket carrier class units to carry 4 gunships for amphibious assualts
*Battleship able to bombard naval/shore targets upto 2 squares away
These changes will make the navy a more potent tool of war, allowing for limited land strikes and support of amphibious invasions, while still being exposed to airstrikes, bombers, and other naval units. Course, it would also be nice to be able to bombard enemy tile improvments, but thats another thread altogether
Of course, to build a good sized combined arms naval taskforce, you would need either unbelievably massive production, or more turns int he modern era to build it up.