The teaching of scripture is to be "in the world but not of the world." It is an interesting balance and one easy to get wrong.
A lot of Christians miss the point by overemphasizing the importance of righteousness and otherness of faith. In doing so they begin to isolate themselves from the world for the sake of purity.
In a sense we cannot over emphasize righteousness, but living righteously in complete isolation from the world is not Christian. A lot of Christians isolate from the world because it is easier to live righteously when you are not interacting with sinners which is exactly against the teaching and life of Jesus.
The key is balance. We need to live in the world but be separate from it. Being "in the world" is as important as being "not of the world." If you lose the balance you have lost being faithful to scripture.
As Christians we may not associate with certain people for the right reasons, but it should not be our tendency in life to isolate ourselves from people simply because they are atheists or people of other faiths.