But by the grace of God I am what I am, and His grace toward me was not in vain; but I labored more abundantly than they all, yet not I, but the grace of God which was with me. (1 Corinthians 15:10)
Only by God's grace are any of us saved. Anyone who hates atheists does so in pride, because they could just as easily be in the same place if it were not for God extending salvation to that person.
15-ish years ago, I was a very active member of a science-themed online forum where I was one of the few Christians and was regularly mocked. Unfortunately, I lacked the maturity at the time to handle it better, and I tended to get into arguments that accomplished nothing (other than possibly making Christians and God look bad). Now, I tend to simply look upon such people with sadness, knowing that are being deceived by Satan and lack the understanding of truth that Christians have been given as a gift from God. But remembering that everything from salvation to knowledge and understanding are all gifts from God should keep us humble, not hating those who are pawns of the devil.