Ahhhhhhhhhhhh, the great debate continues over this subject! My friends and I have had this disscusion for years, and here is my take on this subject from personal experience.
First, there is a "stigma" in some churches that go along with the guitar. I remember being a kid and wanting to play piano. People at the church were too busy to give a kid lessons. Then I gravitated to guitar when I saw Prince and Eddie Van Halen back in the 80's when I was a kid. I wanted to play in the church, but I was told that the guitar sounded too much like "blues" music. Some "churchfolk" still feel this way about the instrument today.
Second is the fact of support for the instrument. I can go into any church and there is a piano, organ, drum set, and to some extent a bass amp. Nothing for gutar! My current church has a membership of 10,000 people, but no equipment for a guitar player. I have to supply my own. Not an issue, but if I have to go out of town or to a different church to offer up some praise, you better believe I am the only on that has to haul his own equipment around!