Missiles firing can escalate the conflict to nuclear level. As the other country will suspect a nuclear attack and chances of misunderstanding and over reaction are much higher. Missiles are for one time use where as plane are multiple use and multirole.
Yep, That's true for ballistic missiles, which goes at extreme heights, makes a parabola then re-entry. They are used for strategic / WMD purposes. The likes of shaheens, ghauris etc.
However, in the next major war the cruise missiles will be used both air-launched and ground based. That is what they are for. Taking out high value targets like air-bases, naval bases, C&C centers, communications facilities etc.
Using cruise missiles or a fighter jets for a specific target depends upon various parameters like where the target is, how much defended it is, what is the risk assessment, what is the available strength of fighters / or cruise missiles available, etc.