Cruise missile are ground units because they can be (and often are) fired from mobile platforms that aren't important enough to be represented in the game, but are implied in the movement of the missile. They aren't important enough because they have no seperate attack abilities. Same for tactical nukes. The only exception to the rule is sumbarines, and that because they actually have other uses besides just missile transport.
Having more types of fighters, ships, and tanks wouldn't fit in with the game. Civ3's combat system is just too simple to really distinguish between such things, and while I think they need to add a cruiser unit, it would actually fill a strategic niche that is empty now. Generic units work far better. Really, the differences between all of the different modern tanks and ships and planes etc. are exxagerated due to the fact that they're in use now. I've rarely see people asking for warriors with clubs, warriors with axes, spearmen with bronze shields, spearmen with iron shields, horsemen with stirrups, horsemen without stirrups, catapults, and mangonels. The reason is because each pair of units fills the same strategic niche. Tactically, they may have great differences, but the differences are minor strategically, and Civ3 is a strategic game, so it cannot accurately reflect tactical and strategic reality at the same time. The first good game that successfully does that will be sort of like a theory that reconciles quantum mechanics and relativity.