True. But there are a number of cases where this has been done. Probably much easier with MARTA tracks, but even with freight rail we have pedestrian bridge examples like Westside provisions, several places between West Lake and Washington Park (e.g.
https://www.google.com/maps/@33.7552533,-84.4378284,127m/data=!3m1!1e3 and
https://www.google.com/maps/@33.7561097,-84.4300411,127m/data=!3m1!1e3, of course the MARTA ped crossings over freight rail tracks (Lakewood, Inman Park, Edgewood, East Lake, Avondale, etc), and dozens of places where PATH trails or other trails cross freight rail. I don't think it's really much of a barrier, it's probably just cost prohibitive and there's no reason for most individual developments to consider paying for it.