It's a shame that the folks at Farecompare no longer participate on Flyertalk so that we could carry on a dialogue with them and help them improve their product. It's still a very useful tool these days but it is far from what it could be. For the time being, think of it as a tool to get a heads up on pricing action with air fares.
The US government needs to require airlines to provide total revenue pricing again. I don't care what the heck you want to call it - you can break your fare down to basic fuel, fuel surcharge, fuel scarcity charge, baggage handling fee, catering fee, whatever; but all of it has to be included in your total revenue figure. This revenue amount should replace the nowadays rendered useless (except to the airline for obfuscating their real charge for the ticket) "base fare" amount.