Because, like large swaths of Southern Nevada, the airspace over Area 51 is restricted. Area 51 falls in restricted airspace R-4808N, and it's not legal to overfly it without permission.
The irony is that the article on the very website of this person who was arrested lays out were you are not allowed to fly drones and urges people to stick to the allowed zones so that the airforce does not have reasons to expand them.
Judging by what was written on your link I assume he was very careful to stick to what was allowed.
All of the airspace nearby Area 51 is restricted too. The nearest unrestricted airspace to Area 51 is 12 NM to the East. It's closer to 30NM if you also want to be near a public road.
The comment does not indicate the drones actually flew over Area 51 (or a military base) : "drones flown over places _around_ Area 51" (emphasis added)
