I was about to book with them on their newly announced flights from Newark to Cancun in the spring and did not because of this same concern.
I see a lot of reviews where this airline cancelled their flights right before and they were stuck in those cities.
If I buy a vacation package (i.e., a hotel resort in Cancun + tickets) and they cancel a few hours prior, not only I will lose my vacation (because the prices for the other airlines on such a popular route in the middle of spring break will be enormous), I will also lose at least some money I paid for the hotel, because even the most generous hotel cancellation policies allow canceling 1 full day before arrival, and more often it's 2-3 days before arrival, after which you lose at least the cost of the first day, if not more.
If they had these interline agreements with the other airlines this would make a huge difference. Because how can I risk like this for a family vacation? I would love to save money, but having this chance of just losing money and not being able to go on vacation at all is too much for me. I did not know anything about F9, saw really good price for the newly announced route to Cancun, but read about these cancellation horror stories and decided not to risk it.