It seems like the Iraqis were relatively poor operators of their systems. A few days ago I was reading about the Nato bombing of yugoslavia on wikipedia and it had the following entry:

"Yugoslav air defences were much fewer than what Iraq had deployed during the Gulf War – an estimated 16 SA-3 and 25 SA-6 surface-to-air missile systems, plus numerous anti-aircraft artillery (AAA) and man-portable air defence systems (MANPADS) – but unlike the Iraqis they took steps to preserve their assets. Prior to the conflict's start Yugoslav SAMs were preemptively dispersed away from their garrisons and practiced emission control to decrease NATO's ability to locate them."

So their SAMs likely just got stealth bombed / bombed from a distance.