I make various pepper wines, including meads. You can use fresh or dried, but I prefer to use fresh peppers. Flavoring honey is probably more trouble than it is worth, considering you could make a basic hot sauce much easier with the same peppers and just throw a few dabs of that into/onto whatever you're wanting the flavored honey for. That said, it doesn't take a ton of fresh peppers to properly spice a relatively large volume of alcohol or honey. You can flavor a 750 bottle of pepper wine or vodka with only 5 good sized fresh habanero, for example. Start small, with the peppers roughly chopped so you can remove all the chunks later. Deseed them first, if you can do so without harming or removing much of the placenta. You can leave the seeds in, but they might leach tannins into your final product and add bitterness. You can get a small, loose weave mesh bag from any homebrew shop for dryhopping (not cheesecloth, the looser mesh) and put your peppers in that to soak. Make sure to push them under the surface of your liquid at least 2 times a day to keep them wet and avoid rot. With a wine base, you can leave them in for a week. With a honey, you're going to have to find the happy place where you pull them out before fermentation starts.
Initially warming honey to 170 degrees will allow you to infuse or mix things with it much easier. Introducing your fruit/spices at this point and keeping that temperature for 5 minutes kills many of the bacteria and yeasts you're worried about (but not all). Taking it over 170 degrees will cause compounds within it to begin to break down. Overheating will lose you a ton of the flavor and complexity of the honey, itself. While initially heating your honey, you can skim off any foam and dump it into the sink or garbage. Those are impurities that the heating process has broken loose. Skimming isn't necessary, but produces a better final product from honey in the raw or straight from the apiary. With the filtered and abused crap on a wal-mart shelf, they've already stripped most of the impurities (along with a ton of the flavor).
The biggest problem I see with making a peppered honey is unintentional fermentation. Unless you ensure the chiles you use are clean/sterilized on the outside, you will undoubtedly be introducing bacteria and/or yeast to your honey. This isn't a problem when making mead, because you already have a brewing yeast culture that is dominant. In something you are not intending to ferment, the foreign yeast/bacteria will take hold unless you store your honey in a refrigerator. This type of fermentation generally won't produce delicious mead or otherwise usable product. As I said, flavoring honey with anything non-spice is in my opinion generally going to be more trouble than it is worth. People who do it commercially are probably using extracts and artificial flavorings, or they're heating their honey past the breaking point to fully sterilize it after infusion.
As to infusing honey with spices, go nuts. The baddies in most spices all seem to be prone to death at or below 170 degrees. Heat your honey to just under or at 170 in a kettle or saucepan on the stove, skim any impurities, stir in your spices & keep it near (but below!) 170 for 5 minutes, then pour the honey into whatever you're storing it in and jam that into an ice bath in the sink to get the temp down to the low 80s quickly. Done. Cheers.
EDIT: wtf did the site do to my paragraphs? lol