Hi Imo,
Which hotel are you going to? It's 9 or 10 stops, depending on which station is closest for you. There is the metro (about 40-45 mins) costing €8, or €14 for 2 tickets, also the dedicated airport bus at €5 a ticket. Both are safe to use, but one could be better than the other depending on your exact hotel location.
The metro stops running overnight (last one approx 30mins or so after midnight), but the bus runs 24/7.
The bus is actually the easiest as the kiosk to buy tickets, & the bus stop, are both right outside door 5 of the terminal, the metro is about 5-10 mins away. The bus also runs more frequently most of the time.
Once you let me know where you are staying & see which is the better option for you, then I'll tell you the process for tickets, there's a big fine if you get it wrong! Don't worry, it is quite simple, but necessary.

In terms of safety,and i can only speak from personal experience,i don't think there's much to worry about,there is obviously crime in Athens,as with any big city and unfortunately some of that will be directed at tourists but it's rare,i've never seen anyone get mugged or anything serious like that,and i've walked the streets of Piraeus late at night while drunk and never had trouble! The only place i've ever felt uneasy in Athens is late at night on Omonia square when there's a lot of Africans walking the streets looking like they're up to no good,but even then it's nothing like 'threatening' or even close and the police are pretty hot on the street people,Yiftis,africans and the like troubling tourists

Just act like you would in London or elsewhere,be alert but not worried,be sensible and just enjoy yourself.