First, your assertion that "everyone is an atom created by the Creator, completely detached from everyone else" is completely false. Christians are joined together as Christ's mystical body (with Christ as head) becoming the one family of God. The church as body of Christ suffer together in solidarity at the hands of our collective enemies just as our head (Jesus) suffered but STILL loving his enemies from the cross, saying: "Father, forgive them for they don't understand what they are doing."
If it is rational for Jesus to love humanity who crucifies him on the cross, then it should be rational for members of his body to do the same. I admire Buddhists who have great compassion to others who struggle in life; whatever their doctrinal explanation. Regardless of one's religion, it is salutary to love one's enemy. I can even see a Buddhist understand the rationale by Jesus said "they don't understand what they are doing", as in Buddhism much suffering is caused by ignorance of our inner psyche. Both Buddhists and Christians wish the best for every human being, enemy or not.
There is an interesting 1996 journal article from the Buddhist-Christian Studies Jesus the Bodhisattva: Christology from a Buddhist Perspective. If for Buddhists it's rational to love one's enemy, it's rational for Christians too, by conceiving an individual Christian to be united to Jesus the Bodhisattva, since one earns the title "Christian" only by being united to the Body of Christ.
But Christians go one step further because Christianity CAN explain the source of that power to love enemies as coming from God Himself which He shares with us through Christ, rather than Buddhism's explanation in terms of Emptiness, as a response journal article A Christian Response to "Jesus the Bodhisattva" says:
However, one might ask on what grounds Keel would maintain that Buddhist Emptiness and God's love (or grace) can refer to the same ultimate reality. ... to say that Emptiness has such a character of grace does not necessarily lead to the fact that Emptiness refers to the same ultimate reality as does the Christian God (or grace). Above all, is it true to say that Buddhist ultimate reality can have an objective reality? If Emptiness is to be regarded as objective reality, it cannot help but be reified. ... As we well know, hoever, such a reifying expression is exactly what the concept of Buddhist Emptiness was devised to avoid. This is because such objective ultimate reality, Buddhists believe, gives rise to human beings' attachment to it, an attachment that must be regarded by Buddhists as something to be destroyed.