That's still cheap when compared to a car!
How much tuning did they have to do?
What does there standard tune up cover?

Tire inflation.
Chain stretch, lube.
Derailer adjustment, shifter function.
Brake inspection.
Wheel runout, spoke tension, hub bearings and pedals.
Skewers/axle bolts correctly tightened.
Cable and housing inspection.
ALL bolts/screws/nuts correctly tensioned.
Thats what my LBS does.
And it takes about an hour.
$90/hr for labor is not out of line.

Ask!