The title pretty much says it all - I've seen rooms listed at hotels such as the Wentworth in Charleston, SC that have two prices, the "Hotel Rate" and the "Innkeeper Rate" which is lower. I've plugged it into Google but found nothing to tell me what exactly what it means. Can anyone enlighten me, please?
Based on the way that rate is presented on the website you pointed us to, I would say that it is simply a discounted rate, that is called an "Innkeepers Rate" ie a special deal offered the Innkeeper himself/herself. Hotels can get quite creative with their discount program names trying to build the perceived value.
Most professional rates, such as the innkeeper rate mentioned in the link in Spehro's post, are not posted on websites, rather they are only revealed to qualified patrons. Many hotels offer special rates to different professional groups: travel agents, airline employees, corporate employees with special contract rates, etc but these rates are never revealed to the general public.
Based on this link, it seems to be just what it sounds like, a rate that another innkeeper would pay when staying there.
It's called "professional courtesy." That is, "Innkeepers" (and other professionals) will often look after "their own." In this case with a special rate.
The idea is to build goodwill to ask for return favors. If I were in a "related" field, e.g. travel agent, or basically anything connected with travel, I would ask for the "innkeeper rate" and show them how I can do them a return favor when they're on my home ground. This might also work for certain other "professions" e.g. supplier of towels to hotels.