Typically it's archaeologists who are doing the defining of what a particular structure fuctioned as.

Determining the function of any structure depends heavily on the artifacts associated with that structure. We have specific things that go with domestic architecture, such as hearths, places to make food, remnants from daily life and occupation, everyday artifacts such as pottery and tools. We also have specific things that tend to go with "cultic" or "ritual" areas such as temples, which include religious iconography, certain religious installations such as altars, certain kinds of artifacts used in religious rituals, etc.

One reason to discount the use of the Göbekli Tepe structures as houses, or domestic architecture, is that they were not roofed, but open to the sky. Not something you would want in your everyday shelter. This can be seen by the type of sediment deposits found both inside and outside the structures. It's pretty clear when a surface is protected from erosive forces like rain and wind by a roof, and the structures themselves are not constructed in a way that would make attaching a roof particularly feasible. So archaeologists take all this contextual information, such as the way iconography is presented, what artifacts are present, what the structure looked like, and they use all of these things to form a hypothesis about how the structure was used. The conclusion based on this contextual evidence at Göbekli Tepe is that it was used for religious purposes, perhaps for burial feasts (though they have not excavated the actual burials yet).