Indeed, there is a lot of very, very bad reviews for Sky Express in TripAdvisor, they all seem to refer to a series of delays and cancellations due to high winds in Santorini last month. They were handled in an unprofessional way due to a bad CS situation at ATH (and, most probably in Santorini as well) due to the fact that the airline uses a handling agent who may not have been contracted for help in such cases (
): typical Greek, in the sense that we tend to never think of unusual circumstances ahead of time. At any rate, I am certainly not going to defend them, if they do this often they'll be out of business pretty soon. The bulk of this small airline's business is flying government-susidized flights between smaller airports and I guess that the ATH-JTR ones are flown in between those.
Now to your situation: 75 minutes is OK, provided your incoming flight is on time. But with only a 30 min. delay on a TATL will make you miss the flight, and since this will be on a different ticket, this will be cancelled and you'll be stuck in Athens. Also, forget about changing the flight from 3:40 to 11:45 at the last moment. It may be theoretically possible after paying a substantial surcharge, given that the flights to JTR are expensive and often overbooked during the summer months. So 4 adults? No way! In your place I would definitely take the longer wait possibility and fly A3/OA.