"You have heard that it was said, 'You shall love your neighbor and hate your enemy.' But I say to you, love your enemies and pray for those who persecute you, so that you may be sons of your Father who is in heaven" (Matthew 5:43-45, NASB).
A few years ago, I heard the evangelical preacher John MacArthur say something like, "It's good to have enemies if they hate you for the right reasons." He was right.
It's a horrible thing for Christians to have enemies because we have been rude, arrogant, or selfish. In those cases, we must repent and ask for forgiveness from those who have been offended. We must strive to refrain from being unnecessarily offensive.
On the other hand, if we are hated because we are trying to do the right thing and honor Christ, we must learn to live with the fact that we will not be able to please everyone. Sometimes honoring our Lord will turn some people off and anger others. It will not be our intent, but it will be the result.
When we have made enemies because of our faith in Christ, it will be okay...as long as we remember to follow Jesus' instructions to love them and to pray for them.