Indeed, we all have and are entitled to our prejudices, likes and dislikes. We are, however, expected to temper them, for the greater good of unit cohesion and out of respect for our fellow man.
For example, I am an atheist (I really am, by the way), who finds most judeo-christian dogma abhorrent and could, therefore, take great exception to the Service devoting resources to religious observance and to having uniformed Christian preachers appointed over me.
The solution: Get over it.