It is a separate €6.50 for 1,760 metres, with no child fare, no railcard reduction and no regional discount. The only reductions are the family rate and groups of 10 or more. A child travelling half-price on the train pays the shuttle in full.
Florence is outside the Pisa comune, so the meter runs on the extra-urban rate of about €2.30 per kilometre on top of the opening charge. Over the roughly 80 km that puts the meter alone past €180 before any extras.
The shuttle's first run is 06:00, and the company ticket office only opens at 08:30. Pisa Centrale's first departures leave around 04:15, so an early flight or an early train leaves you with a taxi as the only way to the terminal.
Two singles are €13.00 against a fixed taxi fare of €10.60 to the same station, and the return pair is €26.00 against roughly €21.20 for two taxi runs. The shuttle only wins on cost when you are travelling alone.