To get to/from Nahuizalco, the alternative to private car and taxis is the bus. Bus line to Nahuizalco is the one which serves the Ruta de las Flores and that goes from/to Ahuachapan to/from Sonsonate stopping in the villages on the way. If coming from San Salvador you shall get to Sonsonate first and then take the bus to Ruta de las Flores.
Buses operate with high-frequency during the day hours two to four times per hour. Price is few cents of US dollar per ride. There is no night service and if you end up staying in Nahuizalco after 7:00 pm most likely you shall overnight.
I did not take the bus and I cannot say whether it is a comfortable ride. I suspect it is not (see photo attached, the service is operated with dismissed US school bus equipment), though I am sure it is an interesting experience.
There is also a minibus service (see other photo attached) which make the same trips in about the same time at about the same rates.
Tourists will likely get to Nahuizalco by bus, taxi or private car. Taxi is a reasonable choice if you have made your base in San Salvador and plan to visit Ruta de las Flores (and Nahuizalco) in day trip and stay only few hours. At time of my visit in May 2007 there were no taxi-stands in Nahuizalco and you needed to have your taxi driver wait for you. I hired a taxi in San Salvador and agreed on a US$10/hour fare, though I suspect I might have negotiated harder.