It homes in on radar systems.
Or spec ops go in and use a Javelin.
Or we hack them like we (or the Israelis) did once.
The S-400 System has a maximum effective antiaircraft range of 250 miles, considerably longer observational range, multiple remote, mobile, selectable antenna arrays, multiple launch vehicles, some of which can launch while in motion, exchanges real time target data with other S-400 Systems, can make a targeting solution and weapons selection in twenty seconds and shares data with S-300 systems.
An attacking aircraft would be at extremely high risk before their weaponry would be in range.
A UAV is much slower with Hellfire's maximum range of five miles and interactive guidance to target.
Likely Trump and our Military's genius in this strike was to keep our aircraft well away from the S-400 and what it is protecting, Russians, not Assad.