I dont have a basis of comparison because I've biked for years and only take public trans in bad weather, but my wife used to take the El daily when we lived in west Philly (moved in june 2020). We've moved twice and she basically refuses to take it alone.

Rush hour is about the only time she'll consider it and even then. Honestly speaking, there's always some risk because some people suck, but it certainly feels more frequent today than say prepandemic.

Eta: regional rail is generally fine.