I have used Gary's Plumbing before and I don't usually mind paying a fee for a Service call because the plumbers go on to fix the problem. I do not think you should be charging to come out and give a bid/quote, especially when the job was such a large one (replacing an entire water line).
As a small business owner myself, I do not charge people to give them quotes. I want their business and will work to get it with solid customer service and competitive pricing.
Though your bid was cheaper, the fee was part of the reason we went with another company.