In my early circuit days, judging the flare was the bit I found most difficult. I was either flaring too high (like a 737) and causing the instructor to reach for the throttle to avoid a sudden catastrophic sink from 15ft, or flaring to low and making my instructor think I was trying to land on the nosewheel.
Curiously I found that because the runway was so long where I was learning (6000ft) I found it difficult to concentrate on the far end of the runway whilst starting the flare. I actually found it easier to look at a fixed point around half-way down the runway, imagining that to be the runway end, as if I was doing short-field landings. That way it suddenly 'clicked' as others have said. Then to my delight, upon my first 'real' short field landing (600ft of damp grass) I nailed it right on the numbers. Still have much to learn as I swear that every landing is different, but then every flight is also a learning experience....
(and before anyone says it, no I don't think that half of 6000ft is a 'short field' - 3000ft is still a pretty damn big runway compared to what I'm now used to....)