What is the best way to get around on Santorini? Should I be concern with travel after dark?
Depending where you are staying, the hotel may have a shuttle from the docks, it is a definite plus if they do, probably worth a little extra room cost. From there, buses will get you to most everywhere easily, as long as you plan your schedule around them. Taxi is a more expensive option. You will also see loads of people on rented four wheel ATV's. Not sure if I can endorse that option, just because most of them seem to be obnoxious and a danger to themselves and others.
If you pre-book accommodation most places will arrange a pick up from the docks. I've never been charged for this, but I mostly stay in small, family owned accommodation. As for getting around, the Greek islands are awash with small independent car hire companies. Usually the cars are parked outside of the shop or on the road. Have a good hard look at them and if you like what you see go inside and agree a price. It's a small island so you don't need to go fast. Drive like a little old lady and you'll have no problems. As for dangers after dark, the only real danger is from drunken Brits falling into the road. On the other hand taxis aren't expensive on the islands.
Book a room when you get to the dock and it will include a ride up the hill. You can take the tram down the hill when you leave. Don't sweat this one.
We were in Santorini last July for 5 days and used a 4-wheeler to get around (I wouldn't let my boyfriend rent a motorcycle even though he has one here). 4-wheelers are so big and slow, I didn't feel in danger at all. We went all over the island on it. When we go back, I'll most likely let him have his motorcycle, now that I've seen what it's like. Just be alert and wear the helmet. Otherwise, walking or the bus is the way to get around.