The Jays don't get less than 11,000 people per game. They were around 11,000 over the last few weeks of the season, but that was a record low. Their average was 23,162 this year. Take away the last month where the team was at its lowest point in recent memory, and that number is probably more like 26k. Still not great, but not bad. It's important to remember that this year the team counted attendance as only paid seats. In the past the jays counted all free and heavily discounted in their attendance figures which really skewed things. Most teams do this, so it's hard to determine how the Jays now compare to other teams, but I'd say they're right around the league average.
I don't think the team is in financial trouble at all. They probably don't make a profit from gate receipts, but they make up for it in other areas such as providing free programming for Sportsnet and the FAN 590. I don't think you can look at the Jays as a sole entity. There's a bigger picture here which is unique since Rogers is one of the few synergies left.
Besides , there's talk that next year's budget might be anywhere from $60-120 million. I think they're going to give Anthopoulos a good budget to work with, probably more than what they had this year, and if they can sign some free agents and get people excited about the team's youth, they could potentially build some momentum in the off-season.