Actually, according to that busschedule website (which I use religiously), you can do that trip in as little as 4hrs on some departures so the time saved may even be more negligible than that. Aside from trip duration the differences are:
1) Price - $37.05 for the shuttle vs. 3910 colones for the public bus (~$7.65 at current rates) plus maybe another buck if you take a taxi to the Caribe Bus Terminal in SJ.
2) Choice of departure times - Interbus has just 1 departure each day at 7:50AM while busschedule.com shows at least 13 different times each day for public buses that will take you to Cahuita. Interestingly enough, in CR "directo" does not mean "non-stop" and the "directo" buses are not always the fastest. Sometimes it is actually quicker to take a "directo" to Limon and change directly to the Cahuita bus there. The bus that leaves at 2:30PM actually is scheduled to take only 3.75 hrs if you don't mind arriving in Cahuita at 6:15PM. The 8:30AM, 9:30AM and 1:30PM buses to Limon with changeover to a bus for Cahuita take 4hrs as does the noon direct Mepe bus. All the others take a half hour longer than that (still no big deal).
3) Pick-up and drop-off points - the shuttle is door to door service, picking you up at your hotel in SJ and dropping you off at your hotel in Cahuita. The public bus runs terminal to terminal (or, in Cahuita's case, the bus stop), so you'll probably at least want or need to take a cab with your things from your SJ hotel to the Caribe Terminal in SJ (though you could practically walk it from the Dunn Inn). As far as SJ bus terminals go, the Caribe Terminal is probably the most modern and safe bus terminal in SJ. At the other end, the village itself is very small and you could easily walk to any of the cabinas there, for places further away (north along Playa Negra) I'm SURE any of them will pick you up right at the bus stop if you reserve with them or else be waiting with a car even if you don't (don't listen to the hustlers and touts who will greet you as you get off the bus and tell you to go to their hotel because your hotel is all full or some other BS like that).
4) Comfort on the ride - personally I find the buses they use on the major routes in CR to be perfectly comfortable for me. The more serious issue is that I would always be much more concerned about keeping an eye on my stuff while on the public bus, however whatever you put in the lower luggage compartment should be fine and your carry-on valuables should be fine too as long as you keep it either secure on your lap or between your feet (do not use the overhead racks).
Here are some map links that you might find helpful:
http://www.moon.com/files/map-images/ctr_03_Central-Cahuita.jpghttp://www.moon.com/files/map-images/ctr_03_Cahuita.jpgThe beach north of town, which extends for several miles, is Playa Negra, a black sand beach. Personally, I prefer white or golden sand beaches. Cahuita's more famous beach is Playa Blanca, which starts just at the edge of the village and extends for a couple of kms along the shore inside Cahuita National Park, however it may be better for sunning than for swimming since it is prone to ripcurrents. A safer beach for swimming (also pale golden sand) can be found even further south from that on the other side of Punta Cahuita as an offshore reef protects that one from the stronger currents. At any of these beaches you need to be very careful about leaving your stuff unattended as theft can be a real problem, so if you go with someone take turns going for a swim or else keep one very careful eye out for approaching people when you go in the water.
If you decide to locate north of the main village along Playa Negra there are 2 clusters of cabinas (~2 and 4 miles north of the main village) along with a few bars in each area so you won't be completely isolated, but you still might prefer to be in the main village to be closer to the main "action" as well as the beaches to the south.
The only "cheapy" cabinas in the northernmost cluster are probably Cabinas Algebra (
http://www.cabinasalgebra.com/en_index.htm) (<$20/nt depending on how low you can negotiate). They're clean and have hot water and fans and even security boxes in the rooms. And their creole restaurant is supposed to be very simple and good. The rest of the places up there are "higher end" than what you're looking to pay. The next closest thing I saw was the Hibiscus Cabinas at $40/nt but FWIW I saw one review on TA that said they were dirty and it ranks dead last out the places listed on that site. The Magellan Inn costs $60/nt & up, so is way over your price point but you might want to at least check out their restaurant, the Casa Creole, for a little fancier creative fare.
Moving closer to the village, in the next cluster you have Cabinas Brigitte (
http://www.brigittecahuita.com/Brig_home_E.html) with rooms starting at $15/nt, clean and hot water like you want but you're not asking for much there. Still they look nice enough. Cabinas Iguana (
http://www.cabinas-iguana.com/Welcome/welcome.html) has rooms with shared baths for $25/nt and bungalows starting at $40/nt. With that you get hot water, of course, but also a really nice looking pool area. The map shows 2-3 other Cabina places in that same area: the Cabinas Jardin Tropical has 2 cabins $30 or $50, The Cabinas Mambo also has rates starting ~$30 and the Bungalow MAlu looks to be even "pricier" than those. For eateries and entertainment in that immediate area, you have the Reggae Bar and the Chao Paradise Cafe and Restaurant, as well as restaurants at most of the various cabinas.
In the village itself, the cheapy place seems to be the Cabinas Palmer (sorry no link or reviews on TA) it has 20 small but clean rooms for $15/nt (sgl) and 13 of those have hot water. Cabinas Jenny on the north end of the village ranked 4th on the TA list, but didn't list their rates. Cabinas Arrecife also on the north side, next door to Miss Edith's restaurant (recommended), ranked only 12th but that may have been brought down a bit by one unusually bad review. Their rates are $20/nt for a single smaller room or $25/nt for a larger unit. On the east side of the village going towards the National Park there seem to be a couple of good budget-priced possibilities: The Hotel National Park ($25/nt sgl or $40 w/a.c.) ranked 10th on TA and the Belle Fleur (starting at $20/nt sgl and ??? for rooms w/a.c.) ranked 8th on TA (but with only 1 review)
BTW, all of the rates I'm giving are the green season/summer rates since I'm assuming you're planning on going sometime in the next couple of months. It should also be noted that since this is the slow season for tourism it might also be possible to negotiate even lower rates, but that would be up to you.
For nightlife in the village the 2 main palces are right across the street from each other - Ricky's Bar for the Jimmy Buffet Margaritaville scene and Coco's Bar for the rastafarian reggae vibe. For cheap eats (especially for breakfast or lunch) there is Soda Priscilla across from the Belle Fleur. And for a somewhat nicer dinner (apart from Edith's creole cooking already mentioned) down the street on the other side of the village there is the Palenque Luisa for "Caribbean Fusion" cuisine and Cha Cha's offering various dishes from around the world.