According to Maria Morris Hambourg, Atget traveled by train and tramway from Paris to the villages and countryside south of Paris*. In her Notes to "Old France" (Volume 1 of "The Work of Atget" MOMA), she says:
"...Atget lived near the southern rim of the city, only a block or two from the Montparnasse and Denfert stations from which the southern-bound trains departed, and not much farther from the southern tramway termini. [...] The railroads that served the southern environs, for example, the Ligne de Sceaux and the Ligne d'Arpajon, were short-haul or commuter lines..." [p.153]
"In Album n 11, environs Atget noted the trains and trams that took him to the villages he photographed." [pg. 167]
Atget also did some early "environs" photos in the countryside north of Paris (Somme), but he lived in that region from 1888 to 1892, so he was not traveling from Paris then.
* of course, if you have ever traveled by train, you know the train station is not often located close to where you want to go, so I'm sure he did plenty of walking, too!