I'm now on the 3rd or 4th campaign and the missiles hitting home are because it is possible to avoid them. I can avoid missiles by changing direction rapidly and hitting afterburners. The enemy seems to do this sort of thing too. It does get better as you get combinations of flying a fighter to eliminate air forces then a dropship to supply ground troops, then taking out an enemy fleet.
There are also gunner missions where you control a gatling gun mounted on a dropship to take out cruise missile launchers, ground troops and other ground and air forces. There is nice variety between missions as you get further in. It also gets considerably harder. The mission I am on just now has me spending three quarters of the time trying to avoid missiles, take out SAMS, drop troops and shoot down helicopters/jets. Give it a bit more playing time. I think you will grow to love it. The only thing I don't like is the fact that by 2050 they seem to have done away with chaff and flack as methods of distracting missiles from homing in on you. Bit annoying having to weave about like a maniac to try and avoid missiles. :grinthumb