Corrected entry: While Ellie is traveling through the wormholes, the chair tears away from the ceiling and then gets thrown toward the ceiling as the pod stops, apparently. The pod was made of man-made materials. Assuming she was traveling at about a bazillion miles an hour, the chair would have ripped right through that pod like paper when it stopped.
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Correction: If you can buy that humans would be able to construct the transporter at all, then you can certainly buy that there may have been some kind of magnetic or force field that protected the physical integrity of the pod. Besides, the film establishes that the events that took place during Ellie's interstellar journey didn't physically occur (if they occurred at all). It's unclear whether the chair was damaged at all after she "returns."
JC Fernandez
The events did physically occur, she physically travelled through wormhole (and therefore she didn't necessarily travel a bazillion miles an hour, as a wormhole is a shortcut between two locations). The real question here is, why did the chair crash against the wall when Ellie and the compass were weightless and floating? Obviously the crash was not caused by speed but just by the magnetic field (it was a metal chair). As such, it would not have crashed through the wall.