Because of the damage and armor types.
And flak dps is split up between 4 guns, arranged on all sides, 90 degree firing arcs. So you have to get all 4 guns firing for them to do their max dps.. usually 2-3 will, or only 1 if yu have them sitting back facing off at the enemy.
LRMs have an overpowered damage type with their high dps.
Flak dps is high, but it's split to 4 guns, and it's damage type is the worst there is.