Plot hole: The snakes are contained in the cargo hold which is shown to be unpressurised on this aircraft (there is an altimeter which releases the snakes after it hits 35000 feet - if the hold was pressurised it would level off at cabin pressure, which is about 8,000 feet). A cargo door is left open to allow the snakes into the passenger compartment, but this would either cause the plane to not pressurise properly, causing everyone on board severe breathing problems if not worse, or would keep the hold at cabin pressure, meaning the altimeter would never reach the right level to release the snakes.
Plot hole: The snakes escape from the locked box stored in the cargo hold when a small explosive bolt detonates and opens the lid. Post 9/11 all luggage placed in the cargo hold of an airliner would be tested for explosives, and anything larger than half a match head would be detected. The chances of getting an explosive bolt on board - nil. None whatever. You can also think of it this way - if the bad guys could somehow smuggle explosives on board, why bother with such an elaborate and flawed plan as letting snakes loose on the plane? Why not just smuggle a bomb on board? Pan Am 103 - the so-called Lockerbie flight - was brought down with a bomb that fit inside a small cassette player.
Plot hole: Towards the end of the movie where the passengers are moving upstairs to the first class cabin, people start pulling down carry-on baggage to blockade the snakes, before the flight attendant thinks about using the raft as a protective shield. You can hear someone calling for the luggage, as well as see people pull it out of the overhead compartments. The problem is that there can't be that amount of carry-on baggage in first class, everyone but the FBI agents and Sean were bumped down to coach, and given how underbooked the flight is anyway it can't be that they ran out of room for it all downstairs.