J.P.
Do you know how old the system is?
Well pumps and pipes, etc. do not last forever and parts wear down over time and with use so it would be hard to say whose fault it is (remember each time you turn on the water the pump goes on).
Either way I think that price is not bad for them coming out in an emergency and fixing the problem. I had to replace a well pump last year at one of my rentals, along with the pipes going into the house. Cost me over $3000 after it was done (they had to excavate to get to).