First, of course, cruise missiles are more expensive, larger, and somewhat more limited in your choice of launch facilities.
The current favorite, BGM-109, (which is, in no way, technologically innovative as SLCM development has been on back burner for three decades) can be launched from a VLS cell in a submarine or surface ship which can also house a SAM or a quadruple of them. There's also no significant technological problem for launching a lot of them from any large strategic bomber or even a cargo plane. Historically the same missiles were also launched from a back of a truck. (GLCM) Compare that to a carrier strike plane which has to be launched from a single carrier with a limited sortie rate, or from a dedicated air base.
As for price, against serious opponents the carrier planes have to use stand-off weapons by themselves and there's no clear price difference between air launched stand-off weapon and a surface launched one. Fuel compartment and engine, after all, are quite minor cost issues when designing a cruise missile. (SLAM-ER costs some 720 k USD versus 570 k USD of BGM-109)
Second, you have to put a lot more ships into action to launch a cruise missile salvo large enough to match what carrier aircraft could provide.
Theoretically yes. A CV(F) is scheduled to launch 110 sorties a day, a Nimitz class a 140 sorties a day, realistically some 125 a day. However, largest part of those sorties are launched to defend the carrier group itself. And as for strikes, largest part of the sorties launched are made to protect and support the strike aircraft themselves (tankers, escort fighters, jammers, SEAD, CSAR etc.).
After three days of strike bonanza the carrier has to rearm and resupply itself and the carrier. In a comparison, a single DDG-51 houses 90 VLS
cells.
Of course, cruise missiles cannot yet handle all the missions carriers strike fighters can but then again UAV's are coming into picture. But for deep strike, carrier is not an optimal tool at all. Technological capabilities for unmanned vehicles are increasing, not decreasing.
Third, carrying the missiles aboard the aircraft lets you devote far more space on the missile to increasing its lethality and far less on propellant expended on its way to the target.
Then again the ordnance carrier strike fighters can carry are rather limited in weight, while, if wanted, a cruise missile can well be size of a fighter (like those Soviet monsters).
Fourth, the time-on-target situation is much better; an aircraft-launched missile can, depending on range, hit its target less than a minute after launch, whereas cruise missiles are likely to take at minimum several minutes to reach their target and can be more easily tracked along the way.
On the contrary. Let's compare two Ticonderoga-class cruisers, each with 50 Tomahawks, and a CVBG. To make 100 strike sorties the Ticos can launch the VLS cells empty within space of minutes. To launch 100 strike sorties a CVBG takes a whole day.
Fifth, it's much easier to carry reloads for an aircraft's missile complement than it is to carry reloads for cruise missile tubes. And you can carry more of them in the same amount of space. And it's much easier to make use of those reloads while at sea.
Yes, but that's a technological problem which could be solved quickly if there was any interest in the issue. AFAIK, most cruise missiles like most missiles nowadays are delivered in their launch cradles ready to be used. Besides, with more cruise missile carries some could be well on the way to replenishment base / area and back more flexibly than in case of a few CVBG's.
All in all, CVBG's are a luxury USN can well afford but I think their usefulness for a medium power is very questionable.