From my evaluations early on in both they seemed like the same thing but VSCode had more features (esp. built-in terminal) and performed significantly better.
I'm sure that there's been a lot of progress in the years since, but I haven't kept up.
I could see not trusting Microsoft with an open source project, but now that they own Github they have two open source Electron-based code editors, and I can't imagine that's going to last for long. So really I'd be more concerned for the long term health of Atom than VSCode.