Depending on your airline (AFAIR there are only two flying ATH-JTR):
- Ryanair: plan two hours
- Aegean: 90 minutes should be enough
Passport control in ATH is fast, if you're from a non-visa country Greeks don't seem to ask any questions except "how long you gonna stay". Expect 15-20 minutes max unless you're unlucky. However since you fly with the luggage, this might take a while, and you can take overall up to 40 minutes before you leave the customs. They don't really hurry there.
Now, if you fly Ryanair to Santorini, you'd have to check in your bag. There will be a line, which will be LONG (because Ryanair asks non-EU passengers get a stamp at check-in even for domestic flights), and checkin counter closes 60 minutes before flight (not exactly, but with Ryanair I wouldn't push it). So you better be there at least 80 minutes before the flight.
If you fly Aegean, however, they only close check-in counter 30 minutes or so before the flight, and they're not busy. They also have a separate bag drop area, and you can check in online (they don't have this retarted Ryanair rule and don't require any stamps). Thus you need much less time.
Security in ATH is fast, and it is max 10 minutes from there to the gate.
PS. Before leaving, check the Greek news to make sure Greek pilots/airport staff/ATC/whoever else are not planning to strike while you're there. Seriously. They do strike regularly. I've been there in Oct when they went on strike, and was a complete chaos, with effect lasting long after the strike was canceled.