can a hero with flying fly over a boulder?

The Fly ability allows figures to ignore obstacles, but not other props. So you can move through rubble, but you can't move through a rolling boulder (that's a trap, not an obstacle, and specifically counts as a wall for movement purposes).

Is there a definitive list somewhere of which props are obstacles?

James McMurray said:

Maybe, I don't think so though (well, there are some buried threads here... including one where I tried to overhaul the props/obstacles/treasure system and tidy it up only to find that it is actually in pretty good order once you examine it closely).
All of the props that came from vanilla expansions are listed in their rulebook under either obstacles, traps or treasure (or 'other props').
The FAQ covers the props from RtL.

So here you go:

DJitD - Pits, Rubble, Water (pg 16-17)
DWoD - Lava, Mud (pg 4)
DAoD - Fog, Corrupted Terrain, Altars (pg 7) Note: corrupted terrain also defined as empty space for the purposes of playing traps (FAQ pg8)
DToI - not clear, all lumped together as 'obstacles and props' so see FAQ (pg 6)
DRtL - as ToI (pg 26)
FAQ - "Sarcophagus", "Table", "Bed", "Fountain", "Throne", "Bone Heap", "Giant Mushrooms", "Tree" and "Ice" (pgs 7 and 12)
FAQ for the purposes of Crushing Block only - Boulder, Crushing Wall, Rubble, Water ... and only these (pg 11)