That bus company website was kinda interesting but, since he was asking about taking a bus to Manuel Antonio and not just Jaco (or, for that matter, catching a bus from the airport), he might find these more generalized websites to be more useful:
http://www.thebusschedule.com/cr/index.php
http://www.visitcostarica.com/ict/paginas/LEYES/pdf/ItinerarioBuses_en.pdf
and for the official fares:
http://www.aresep.go.cr/docs/Tarifas%20Vigentes%202009-12-11.xls
It is not as easy to look up fares on the new xls format as it was on the old pdf one but the latest fare for the express bus to MA is now 3700colones.
As for ID's comments, as usual, he is pretty much on the mark.
I would really not worry about robberies at all on primary routes like SJ>MA or even that much on the more local routes. Does it EVER happen? Sure. Does it happen with so much regularity that you really need to be that concerned about it? Not IMHO. A much more valid concern would be THEFT of personal articles while you're not looking or are otherwise distracted both on the bus itself but particularly while waiting for the bus at the terminal. But that is nothing that can't be reasonably controlled with a little bit of alertness, a dose of common sense and simply keeping your valuables close and secure. Most of us probably actually face a much bigger risk of robbery when we walk around the Gulch.
Also, like ID said, there are no bathrooms on the buses. If you take care of business before you leave that should not be a problem on the shorter trips. On the longer trips the buses always stop for bathroom breaks somewhere along the way. So I wouldn't worry too much about the lack of an on-board bathroom either unless you or your chica have some sort of bladder problem.
Finally, as to A/C, I have also heard the complaints that the international buses (which do have A/C) can be so cold that they're actually uncomfortable. Personally, I have been on some that might have been a little too much on the cold side but none that were really that horrible. But that could just be me. We all have our own comfort levels. On such routes, it wouldn't be a bad idea to bring a heavier shirt that you can layer over your t-shirt or jersey just in case.
OTOH, the local buses, like the one you would take to MA, rarely if ever have any a/c (at least none that works) but again, at least for me, I have rarely found that necessary. I always try to get a window seat so that I can enjoy the views and have found opening them up to catch a breeze usually keeps me cool enough. The outside temperatures may getter hotter once you get down to the coast but the roads there are also straighter which means the bus can go faster resulting in even more breeze through the windows to offfset it. The only real problem that ever occurs is when it starts to rain and you need to close the windows to keep from getting wet. At those times, the bus rides can get a quite muggy. OTOH, the bus route from SJ to San Isidro can get QUITE cold and clammy even WITHOUT an A/C because that route passes up over the Cerro de la Muerte, a high altitude cloud forest area. However, for your route I wouldn't worry too much about the lack of a/c either, particularly at this time of year.