Well, according to President Obama, we are not a Christian nation, we are a nation of values.
But In response to your question, perhaps it is because all those claiming Christianity are not Christians in the sense taught by Christ. Of course, even the beginning churches consisted of the same types of folks and the apostles had to contend with the same issues of racism, sexism, segregation and so forth.
As long as we have imperfect humanity, we will have imperfect everything. What some people claim and what is true can be two different things. Some, like the Apostle Paul before his conversion, are sincere, but wrong, others are plain hypocrites, still others separate themselves over doctrinal disagreements such as is happening in the Catholic and Episcopal Church at this very moment. Reasons goes on to include pride, power, etc.
Bottom line: The wheat and the tares will all tarry together until harvest day when real separation will occur.