Offred and Ofglen are both looking into a store called Soul Scrolls, where prayers are printed out and spoken aloud, and the paper then recycled, all by machine. These prayers are recited without any human element.
When Ofglen asks Offred if she believes God listens to these machines, Ofglen is, literally, questioning if the prayer of a soulless machine can have the effect of the heartfelt prayer of a human with a heart and a soul. However, and more importantly, she is daring to be subversive. The state has decreed that this is an effective form of prayer. Therefore to question it is treasonous.
Ofglen is showing her disrespect for the regime of Gilead by the question. She is also stepping over a line, reaching out to Offred—taking a risk. Their eyes meet as they stare straight into each other's reflections in the glass of the Soul Scrolls store, and as Offred notes, she could easily turn away and cut off Ofglen's question. But she does not. She simply says no, she doesn't think God hears these prayers, joining Ofglen in her treason.
The importance of the quote centers not on whether or not machine prayers can be heard by God, but on the fact that by asking the question—and getting an answer from Offred—Ofglen establishes a real connection with a fellow handmaid, another forbidden action in Gilead.