As one reads history books, one thing that continually disturbs many people is the role organzied religion has played in conflict. To many people organized religion is associated with intolerance, cultural extermination, and a host of other downfalls. As people search through eastern spiritualism or indivualistic new age spiritualism to replace organized religion they often tend to get caught up in a cycle where the problems of things with which they are familiar are obvious, while those of the pristine foreign cultural mining fields are pure and undefiled.
While one can attempt to defend organized religion by appealing to the advantages and disadvantages of other quasi-religion philosophies, eventually this just results in unproductive dogmatic boxing. So perhaps the better question is, knowing the propensity for possible abuse in tightly controlled hierchial buearacracies, why would God choose to use this venue?
A few possible answers come to mind.
1. It prevents individuals usurping authority and proclaiming themselves as a source of truth. Thus the organization helps prevent people from having to choose between innumerable competing voices. Of course this may mean a reduction in efficiency as fulfilling the needs of a large diverse population necessarily means individual exceptions are harder to accommodate, and thus, eventually harder for the general population to accept.
2. Related to the last point, it may be the best of a series of compromise solutions. When one considers the individual benefit times the number of individual likely to benefit, institutions are a natural maximizing outcome. While individualism may maximize what any individual can get from readily available sources, it does not mean that a large population will cummulatively be maximized in a similar way. Often a single capable individual can assist a number of incapable individuals, even if the method of transfer isn't perfected tailored to those on the receiving end.
3. Our natural propensity for religion is a seed in human nature around which basic governing structures can evolve. In this sense, people have a strong inheritied tendency to want religious like uniformity within their group. In this way organized government would have evolved as a watered down version of orthopraxy.
4. Perhaps our tendency to organized religion is an associated consequence of our tendency to institutionalize successful practices or strategies. Of course this is precisely what those who argue for individualized spritirualism state. Proponents of organized religion consider this tendency beneficial, while detractors consider it limiting or oppressive.