Took the public bus to Jaco last week, for the savings as well as the experience.
It wasn't bad at all. We bought the tickets the day before at Coca-Cola bus station. When you buy a ticket you get a reserved seat. We didn't notice this, and took a seat in the back and had to relocate to our assigned seats when the people who had those seats came on.

I never felt threatened or saw any shady characters. I did take the appropriate precautions: kept my stuff with me, not under the bus or in the luggage rack above. It wasn't an issue. There was a bunch of young guys playing music, like a party.
The only bad thing was no A/C and no bathroom. The open windows do provide a nice breeze, which can be good or bad. Good when it's very hot near Jaco, but very bad when you get closer to SJ and it turns dark and cold, and you get the "gripa".

(I came home Sunday sick as a dog). If you get the urge to piss, you may be in trouble since the buses only stop to pick up/drop off passangers. We did make a 10-minute stop on the way to Jaco about 45km away.
I will probably not take the public bus again. Not that it wasn't good but because it becomes uncomfortable after 2 hours.
And since I'm never going to Jaco again, everything else is further away so I'll fly or take the tourist vans.
The price is unbeatable. At 1,355¢, or $2.63, per person each way, it's $10 for 2 people round trip versus almost $70-80 for the tourist vans.