Simply said, the film features four stories about four different generations of gay men, and each is represented by one of the four main phases of the moon.
Sergio Tovar Velarde, the director, explained the title to the blog QueerGuru:
QG: Was it an important element to you that each of the four stories end on such a positive note of hope?
QG: Yes, and that is why I chose Four Moons as my title. The moon has a life cycle and resets every month, and then there is a new moon. When there is the moon it is the night and there is darkness. For a very long time gay people had to be hiding in the dark, otherwise they would have to bear too much pain and suffering, which I believe is not the way it should be. So pretty much the film has four different types of moon, and the last segment is the dawn where the sun is rising up again. Even though they are still ‘dark’ places such as Uganda and Russia where life is really difficult for gay people I really believe that this is an evolving world that is allowing us to lead a better life. I believe this is a new era full of hope, and that the future is bright for all gay people, and is changing as it did so in the past for the black community and for women too.
It’s important to me to say that good times are ahead and that we are approaching an era of better understanding, of better sympathy for each other, and a world where the small detail of who you go to bed with will not matter anymore. I believe we are approaching the end of the night for gay people.
He says the same in this interview on YouTube (h/t Ankit Sharma):