Many took the central premise of the very US-coded humans fighting against religious, fanatic genocidal aliens that way, especially after Halo 2 introduced the religious leaders of the Covenant called the Prophets, the leader of them being the Prophet of Truth. Also, the Arbiter, an elite warrior working for the Prophets was called Dervish during development. Halo 3 introduced a mechanic where cornered enemies would try to suicide bomb you. Also its revealed that the Prophets' religion is false and the humans are secretly the gods they worship and they're trying to cover up that fact by killing them

For context, Halo 1 came out in 2001 but Halo 2 came out in 2004 and the aftermath of 9/11 and War on Terror was in full effect. Halo being islamophobic is a common sentiment on Hexbear and while I think it's a bit overblown you've got to understand how it looked at the time

Space islamophobia

Basically what the reply above said. Still recommend giving the original trilogy a shot though, they're fun.