As far as we are concerned there are no bad times of the year to go to Mexico however many would disagree with us. There are rainy seasons and the summer is extremely hot. During the rainy season it can rain every day and there is the chance of hurricanes and other natural disasters that affect the Yucatan.
Playa del Carmen and Chetumal have been completely wiped out in the past and what you presently see are rebuilt cities. If you wonder why you see dilapidated buildings that nobody seems inclined to repair or demolish consider the circumstances. The hurricanes will return some day.
Flying to the Yucatan depends largely on the weather. Not in that it affects actual flying there any more than the weather affects flying anywhere, it is simply that charters do not fly into Cancun during the off seasons. Flying to anywhere else in the Yucatan most likely means flying to Mexico City or Cancun first.
Some flights from Canada in the off season must fly to a USA city first, then transfer to a flight bound for Cancun or Mexico City on an American airline. Flying from a city in the USA means first flying to a city on the flight path to Mexico then transferring. The cost of flying is also higher in the off-seasons because you are not taking a charter flight.