That’s a good question and the explanation is partly historical. As the church grew and spread all over the world, it began organizing itself in different places, and although each one was to be the same as all the others, differences developed.
Some churches separated from others over doctrinal issues. That is, some felt that parts of the church began teaching heresies-things that were not true. This eventually brought separation. A major split occurred in 1054 between the Eastern and Western Church, resulting in the Eastern Orthodox Church separating from the Roman Catholic.
The Reformation of the 16th century saw the formation of Protestant and Anglican churches, and the Anabaptist movement resulted in the formation of evangelical churches, such as Mennonites, Hutterites and Baptists. Later on came denominations, formed because of different national churches or differences in doctrines. The church has kept subdividing ever since.
Today, the diversity of churches is less about division and more about diversity of spiritual expression. New generations of believers are looking for unity across the denominations and are breaking down the barriers between them. Despite some doctrinal differences, there is more agreement than ever before on the foundational issues that link all churches together as a body of believers.