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Travel within Costa Rica - buses and shuttles?

My husband and I are traveling to Costa Rica in March. Before a guided trip, we are traveling 6 days on our own. We don't want to rent a car, but the US State Dept website says US citizens travel in CR should not travel by public bus (!!). Is that true? We had hoped to combine some bus rides with taxis and/or private shuttles to get to a few accomodations. For example, San Jose to just north of Jaco, and Jaco to Zarcero, north of San Juan. What is your experience with buses (in and out of San Jose), and are there shuttle services that aren't 100% private drivers that you would recommend? Trying to keep expenses reasonable. Thanks.

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We have no experience with public buses. We used Morpho Shuttle three times and were very pleased with them.

We just returned from our second trip to Costa Rica. We flew into San Jose Airport and took an expensive taxi ride to Quepos/Manuel Antonio Park Area. We took the local bus a few times to Quepos to get some groceries and go to a farmers market. Bus system is very good and cheap. The drivers will even give you change if needed. We decided to take a bus from Quepos to San Jose to meet friends. Excellent - very cheap, air conditioned, very safe. We had to buy our ticket beforehand from the bus station.
Buses run from Jaco/Hermosa to various places. Also very cheap and safe but not always air-conditioned.
Taxi Service from SJ to Quepos area/then from Jaco to SJ airport: we used Bryan's taxi service and would highly recommend him. We used What's App to book him (506-8523-3025).