• Requirements.  Have you provided the best requirements possible?  You want a lighting control system but have you clarified how much control and the types of lighting?
• All or Nothing.  Did you hand them a sheet that said "we want a sound system for our church that does everything?"  If so, they will give you a price to meet that need.
• Flexibility.  Do you have to have "top of the line" products or will a mid-range component fill the need?  You might want that cool $5000 sound mixer but a $1200 one might do just as well given your use of it.

A proposal is often a starting point.  If you find a contractor that you like but their proposal dollar figure doesn't fit with your budget, look into these areas and I'll bet you will find a way to provide better requirements and thus receive a better proposal.