There is one regional direct flight per week with Satena, it’s a 1h10 flight leaving on Sundays at 12:35 and arriving at 13:45 (around 52€ single trip).

You can take a bus (10 hours – 520 km), the way through Neiva is safe and there are beautiful sights on the way, like the Tatacoa Desert or the Magdalena River, the most important of Colombia. The bus goes to Pitalito, and most have AC, toilet, TV, but make sure you take a direct one. From Pitalito you can take a taxi (50.000 COP) or a minivan or pickup (~5.000-15.000 COP per person depending on the comfort level). The night bus from Bogota takes a few hours less due to less traffic, but make sure you take a direct one. There is a bus that will take you direct to San Agustin and stop at the city center (69.000 COP). You can also fly from Bogotá To Neiva with Avianca, LAN or EasyFly, and then take a taxi to the Terminal de Transportes where a high variery of transport options are available to Pitalito. Seats in the minivans are assigned, so make sure you know which seat you are getting, and that you are taking a direct vehicle that will not make any stops. 

There are several direct buses, it’s a long 5 hours bus trip (135 km) of which roughly 50% is unpaved and very bumpy (33.000 COP).

Take the jeep leaving San Andres at 6.30 a.m. or 8.00 a.m. to Plata (1,5h 10.000 COP). From there you can take a minivan to Pitalito at 9.00 a.m. or 12.00 a.m. (3h, 18.000 COP). From the bus terminal in Pitalito are regularly leaving shared taxis to San Agustin (45min, 5.000 COP)