Geometric thinking challenge
First of all, introducing flight turns the pseudo-twodimensional problem of navigation in fights (it can include height differences already, so it is not 'flat') you see on the map into a problem of threedimensional space out of necessity.
Thinking in 3D is hard. Instead of having to think in squares that have an allocated height over others (like the top of the stairs being 2 yards higher than the foot), one is prone to start to think in coordinates over 5-foot-side-squares or cubes in which people are. But, is that correct? The rules stay silent on this (as I will show in a minute).
Now, basic thinking challenge out of the way: can a creature fly while the cube(s) they occupy have their own base level in contact with the ground or any other impenetrable surface?
What do the rules say?
Let's look into the combat rules! Terrain and Obstacles tells us:
Flying and incorporeal creatures are not hampered by difficult terrain. [...] Flying and incorporeal creatures are able to avoid most obstacles.
Then again, Trip mentions fliers:
Some creatures — such as oozes, creatures without legs, and flying creatures — cannot be tripped.
And that's it. No more word on fly, flight or flying in this chapter.
Nothing in the combat rules (where all the movement stuff in combat is introduced) contains any real substantial change to the ground combat rules, actually the fly skill doesn't introduce any solution to the Geometric thinking challenge (occupied Area with a flight level vs. occupied cube(s)). But is it neccessary to answer the question if one can fly on ground level? Do the monster feats Flyby Attack, Hoved and Wingover give more insight?
Sadly, the rules themselves don't tell a lot about how to handle the 3D problem of airborne combat, but in either way, none of these rule snippets I could find does rule anything about flying or hovering at close to ground level.
Interpretation of the finds
I can not find any rule preventing flying at ground level or close above it, in fact, the notion that rough terrain and most obstacles can be ignored and that fliers can't be tripped strongly hints, that the Devs thought at least some about airborne people on or close to ground level. The exception to terrain and obstacles can be easily read as "flying creatures can be close to rough terrain and obstacles and still cross them unhindered because they fly".
Applying reversibility to the last statement (which is a slight logic leap) it becomes "flying creatures can cross rough terrain and obstacles, even if they are close to them". This seems to imply, that there is no lower limit of where a creature can fly (as long as they don't try to clip through the ground). So it might answer the question:
Under strict reading, nothing prevents an airborne creature from flying or hovering as low as it wants (as long as it is not clipping through the floor while not being able to do so by different means too). Calling in interpretive reading, the rules even seem to imply that low level flight is intended.