I'm no pilot, but I'll side with them on this issue. Engineers build a plane with a certain fuel capacity for a certain distance, pilots carry what they feel is sufficient to get them there and then some, based on that spec. An airline might have an opinion that the flight could be accomplished with less fuel, owing to new wing tips or some other kind of design change. Opinions vary, that's why we have so many of them. Pilots following design specs on aircraft should not be punished.
I bet the pilots getting dinged for this are old pilots. There's a reason why they're old pilots.