The first usage of militant atheist out there is in quotes. Which clearly indicates that the author doesn’t actually believe that’s an appropriate term, but is

The first usage of militant atheist out there is in quotes. Which clearly indicates that the author doesn’t actually believe that’s an appropriate term, but is rather saying that if what is described by some as militant atheism (an adjective the author doesn’t agree with, hence the quotes) then all scientists should be atheistic enough to be described as militant by those people.