With the caveat that I'm still fairly new at this...
I live west of San Antonio in Kerrville, in an area with no local rail activity.
My experience at SAIT was moderate - although I was on public property, outside any fenced or signed area, we were still run off by UPRR security people after about 15 minutes. Rather than create an argument or confrontation, even though I was well within my rights we left the area.
Better experiences by far were along the Del Rio sub, which roughly follows Hwy 90 from San Antonio to the southwest. Good spots along that section include D'Hanis, Knippa (excellent) and Uvalde, with a number of good, safe and public spots along Hwy 90 itself that offer views of some of the trestles.
There is lots of MOW activity going on, with good shooting opportunity of the Plasser-American gear, particularly in D'Hanis and Knippa, as well as the siding at the Vulcan rock plant in Knippa. All the UPRR crews I've met have been friendly. D'Hanis and Knippa both have safe parking locations, with good vantage points off railroad/private property.
There is also a platform in Hondo, this is an OK location to catch the passing intermodal and manifest traffic, although it moves past this location at a pretty fair clip - better for video than still photography.
I don't know much about central San Antonio's yards, but I think there are a few others here who do...