Something tells me you are new to this game.
Use your Apaches from great distance. The enemy can't have complete view of the battlefield. The Apaches can go behind hill, sneak, fire and cover. Use trees, hills, buildings anything to take cover and you should be able to do it. I know it is possible, I do it all the time.
The only way for non manpad infantry to hit your gunships is if you are flying too close to it. Don't use your apache like an inf squad. Have it at least 40 hexes away from the enemy units.
Javelin and top attack tow can not be innefective against T-90. They are top attack missiles, most of the time they hit a tank, they will destroy it. I don't know how you see them as not effective against T-90.