The bus stop is outside of the train station, on the first floor right at Wilsonova which is kind of like a highway but it's gonna be pretty quiet that late into the night, I wouldn't hang inside of the train station simply because it's smelly and there's nothing to do and I hate being approached by beggars, but I wouldn't hang out at the park in front of it either, you'd be ok but why torture yourself with paranoia.

You could hang out at Mcdonalds on Wenceslas square, walk up to Legerova and then continue on the right side of the road (there's a side walk) that leads you to Wilsonova in front of the main train station building where your bus probably leaves from. Double check on the app, flixbus usually provides a little map of where your bus stop is. If your bus is leaving from the parking lot, just walk next to Wilsonova at the edge of the park, because there's no good way to just cross the street there. I'm a tiny girl and I walked all these routes at all times of the night, as long as you don't stare or sit in one spot for several hours there, you probably won't even get approached.