Because they were smart.
Religion should be kept within the confines of your home and implemented in your behavior and benevolence towards others.
When you make it political and you start shoving it down everyone's throat by force just to conquer more land...it ruins it.
That's not entirely true. Though religion is one's personal choice; however, its' implementation becomes a way of life when you decide to become a faithful anything (whether it be Christian/Muslim/Hindu/Buddhist/Atheist/Jew). Religion, in its core, and specifically Islam is a complete way of life. It is not simply a ritual to be performed at convenient times as a matter of routine to satisfy the inner urgings. It requires a overhaul of priorities, and way of life, and if done right will make you a complete human who lives upto his/her full potential while serving the humanity, thus becoming an example and ambassador of the faith. i.e. Prophet Muhammad and companions for Islam. Buddha for Buddhism, Jesus for Christianity/Islam, Moses for Judaism/Islam, and so on...
You are right however, often folks who are meant to be conveying the message of religion, instead turn to "use" it for their personal agendas and worldly gains which then leads to the mislabeling of the good name of the religion which they still pretend to preach, not realizing they've gone far from its teaching the moment they sought to use it for anything other than to gain pleasure of the Supreme Creator, the One God.
An organized religion is a community at-large, and it is a beautiful thing to have when every member of this community fully understands his/her role, knows his/her faith and its origins, and wills to live according to it, and work within the bounds of humanity for the sake of earning everlasting pleasure of God and be victor in the hereafter. I believe an organized religion in itself is never a bad thing, but when bad elements of any organized religion becomes its voice and are seen to be its leaders, then the community as a whole is in trouble because suddenly their so-called "representative" is the worst of their kind according to their own teachings, and thus projects a negative image of the religion itself to all others.