In Matthew 5:44 where it says "love your enemies" what is covered here? I mean can enemies be muslims or atheists? Is there any restriction to the meaning of "enemies"?
In short, no, there is no restriction.
However, I don't believe this implies that we need to literally have a 'list' of enemies, and then love them. I believe it's God telling us that everyone requires love, understanding. If you show love, you can't have an enemy.
Once again, we as human beings fall short, thus require Jesus.