Some of the aircraft flown by the USAF and the US Navy have higher annual operational costs than the sticker price of those same aircraft. The F-35 is an attempt to avoid repeating the same mistakes, but obviously, easier said than done.
Buy a kayak for $100? You need around $100/yr in storage, cleaning and upkeep for it.
Buy a glider for $10k? You need around $10k/yr in maintenance, hangarage, taxes, insurance etc.
Buy a jet for $1M? You’ll spend that much on a hanger, crew, fuel, taxes, mechanics, parts, insurance etc etc.
Get an aircraft carrier for $1B? You’ll spend that much on crew, ports, maintenance, munition, training etc etc.
Sure you _can_ do it cheaper, but it’s a good rule of thumb from a budgetary point of view.
I think that if nothing else is learned from this program, it's that 'cost estimates' regarding it fit someplace between 'meaningless' and 'fraudulent'.