There's been heaps of previous threads on this topic,
there are many problems with commerical honey, for starters in some cases they pour antibiotics into the hives (which can lead to antibiotic resistance in humans that eat the honey)
They also harvest all the bees honey & replace it with sugar water (greedy greedy) but apparently this can weaken the colony.
I've also heard they kill the queen bee every year or something?
Not many people in Australia have heard of Colony Collapse Disorder, its big in the US at the moment to the point where farmers have to hire hives from across the country & they get trucked to their crops for pollination.
They say causes are unknown but experts speculate , GM foods, pesticides etc & other issues associated with the commerical honey industry have caused the problem.
Its hit Australia & its possible it could become an epidemic.
http://www.youtube.com/watch?v=unca1QR3nLs
No bees= no pollination= no fruit/veg= no man!
I eat honey occassionally but only from my Uncles farm, he has one hive, amidst his property of fruit trees & doesn't use antibiotics, he doesn't kill the queen or any of the bees & he only harvests some of their honey occassionally, & the hive still thrives, so I don't have a problem with it.
I also plant lots of bee friendly trees/flowers/habitats etc in my garden to assist them! we have thousands of bees in our yard on a regular basis, nearly all of our trees/shrubs are the flowering kind