If you download the pdf schedule at the link you provided, you will see three bits of 'rider info' that are applicable:
- When flagging a bus along the route, choose a
safe location where the bus driver can easily
see you, can safely pull off road and where you
are not at risk from other vehicles.
Ok, so you can flag the bus, you don't have to get it at an official stop.
- Signal bus with a two-handed wave. Check the
destination sign to ensure proper bus.
Be obvious when flagging it, a subtle gesture isn't going to attract attention.
- Let driver know where you will be stopping, or
when available, pull the stop cord near your
seat prior to your requested stop.
Similarly, you can get off between 'official' stops, but let the driver know you are going to do so reasonably early.
As an addition, I will note that it is pretty clear from the full schedule that several of the buses don't go all the way to Cannon Beach - in each case the return trip starts 20 minutes after arrival in Manzanita, while Manzanita to Cannon Beach is 25 minutes one way on the schedule. So, only 4 of the 6 buses go beyond Manzanita to Cannon Beach (or can be caught between Cannon Beach and Manzanita going the other way).