You sure you saw flights from Belize to Cozumel, rather than to Corozal? But then $1000 doesn't add up. It's US$82 return SP - CZL, with the journey as per above.
There was / is a Canadian airline flying from Toronto to Cancun and then on to Belize, but it seemed a sketchy schedule at best, and the guests we had do it could have got off the plane in Cancun and caught the bus and arrived at about the same time as they did flying, due to ground delays in Cancun.