We only got on the tender at 10am because they shut down the port prior to that, we got on the Oia speedboat at around 11. There was a short line at the ticket office (with the sign "Transfer to Oia" at the end of the dock), but it's nothing like the long cable car line we walked past. Once we got the tickets we were able to get on the first available boat which didn't take very long to arrive. We suspect not as many people knew about this option since it was not advertised by any crew members (to sell more excursions I guess!)
There was a bus at the end of the boat ride that took us up to Oia town. We ended up exploring Oia for 2 hours before getting on the hourly bus ride back (at the same point where they drop you off).
Also, they do take credit cards but it seems like they would much rather have cash, so just be prepared for that.
We ended up walking down which went better than I expected. The line was 1-2 hours long as the other poster mentioned.
It was weather related, choppy seas on the way to Athenios I suppose. We noticed the occasional choppiness on the boat ride to Oia but nothing major.
Thanks for sharing! Sorry to hear about your experience, seems like the speedboat we took was the way to go especially when multiple ships are in port.