pyhsics question, if a train pulled into a station and stopped, the doors opened and a bird flew in and?

If the bird is trying to hover, the accelerating frame of reference of the train would cause the bird to appear to be accelerated to the back of the train unless it landed or flew to counter that force. The air is going with the train, indeed, but that feeling of being pulled to the back as the train accelerates will apply to the bird.

That being said, the bird would probably figure out what is going on rather quickly and stay with the train by landing or flapping its wings.

The birds location when hovering in the air would remain at the same point. The train would be moving around it. But with that said it wouldn't take more than a few seconds for the bird to compensate with its flight patterns

It would move with the train because all of the air in that cabin is moving with the train as well. Think about it; If you were sitting in a train, would you feel wind when it was moving, if no windows were open?

The bird would accelerate to 88mph (regardless of species) and appear outside the train as though it had never entered it, only carrying a sports almanac this time.

Its about the frame of reference.....