Well, if you have a modern sewage treatment plant it is possible to recover phosphate and ammonium (NH4+) as relatively pure chemicals at the end of the process prior to releasing the treated water back into the environment. It's a bit cost-intensive to do this however, but it might make economic sense as fertilizer scarcity grows, especially for the phosphorous fraction.

But yes, applying untreated human feces to agricultural fields is a very bad idea from the infectious disease and parasite transfer perspective. Also, many sewage streams have additional contaminants (heavy metals etc.) from industrial sources, and varying levels of pharmaceuticals of all kinds.