I'm looking for a bus from San Pedro de Atacama to Antofagasta, Chile in September 2013 I found a bus company but looks like there are no buses in September. Do you know any other bus companies who operates in September on my route?
There are buses. At the very least, you can get a bus 1.5 hours west to Calama, which has a bigger exchange. A member of our party did that in August (winter) and got to Antofagasta, Iquique and more.
The bus companies in Chile/Bolivia don't have much online presence - it's far easier to just get one in the town - but go as early as possible when you know when you want to leave, gives you more options.
Indeed, as per Wikivoyage, there are many daily arrivals into Antofagasta from both San Pedro and Calama.
If you are arriving in San Pedro after a Salar De Uyuni tour, ask your tour company as they can often book ahead for you. Members of my party did that with Tierra Mistica - the company we used for the salt flats.
In general, after 4 months travel in South America from July to November, the only place I could really book online was in Argentina - everywhere else I just did it at the bus terminal in each city, and never had a problem finding some sort of bus.
My English is not so good but you can seek for Turbus buses. The bus company covers all Chile ;-)