Good question! According to http://ksoutdoors.com/State-Parks/Locations/Prairie-Spirit-Trail:
A separate per-person trail pass is required to use the trail for persons 16 years of age and over, except in the city limits of Iola, Garnett and Ottawa. $3.50 self-issue day permits are available at trailheads. Annual permits are available for $12.15 where KDWPT licenses and permits are sold.
So yes, it’s a per-person fee, and not a per-bike fee. There are self-pay envelopes at most of the trailheads; just fill in the info (bring a pen if you can, as these often disappear), put your money in the envelope, and drop it in the lock-box, keeping the tear-off portion as a receipt.