I prefer to fly, even if it takes slightly longer. Trains in EU are usually more expensive. Central railway stations are occupied by criminals and homeless. I would not dare to use toilets there.
This is very different when it comes to airports as even small tier 2 airports are somehow clean and safe due to tightened security of them being airports and not train stations.
I live in Dresden. Could you elaborate on what you find unclean or unsafe about Dresden Hbf? I travel from there quite often, and don't recall any experiences that would make me feel unsafe or uncomfortable like you seem to allude to. If anything, the one thing I notice is that there is the high density of police patrols, since the border police for trains going to Czechia and Poland operate out of Dresden Hbf.
It's not like I've never seen a homeless person in a city center (which includes train stations, though usually they're not inside) but I'm not sure that crime rates are actually that high. With cameras all over the place, it sounds like it would be a hard place to operate at more than a handful of times until they know what you look like, but IANAC.
Airports are much better! No squatters, beggars or drug dealers!