I don't know why it is, but there seems to be a certain resistance that many people in our field have to considering ourselves professionals, deserving of the same rates that other professionals charge and subject to the same types of standards that other professionals have.
If IDEO were charging $5,000 for the same thing, I don't think many traditional product designers would complain; they'd simply wish they could afford it or ask their companies to send them.
In technical areas, the courses are generally cheaper. For example, one day of SIGGRAPH tutorials costs $375. Of course, there you really are buying a tutorial from experts, whereas here you're probably buying networking as much as anything.
For perspective, we had a marketing workshop here in Edinburgh that basically offered intensive, MBA-level instruction on marketing. It was taught by a former head of marketing for a major North American firm who had buckets of experience and now has his own major marketing consultancy here in the UK. Around a dozen of us worked with him for 8 workshops and had three extended consultations with him about our particular business circumstance. The cost to the company? £750 ($1200 USD at current exchange) for the first person, £500 ($800 USD) for each additional. Consequently, unless these three amigos are going to ensure the success of every company who signs up, I fail to see how a price tag of $1000 is justified.
[1]http://gettingreal.37signals.com/ch07_Meetings_Are_Toxic.php
An amateur logo designed for your business.
FTFY
I've run technical training sessions that cost this much before, and I think everyone in the class felt they were worth it.
Psychological studies have been done that people who pay for something - anything at any price - always look more favourably on it than those who do not. One such study involved payment to see a film. Those who paid their own way ALWAYS had more favourable reviews of the film than those who were provided with a ticket for free.
Obviously, there is a limit to the psychology, but I wonder how much the feelings of a class' attendees can viably count toward evaluating the value of the workshop. Price is naturally where the willingness of the buyer to buy meets the willingness of the seller to sell, so the price of the workshop is beyond dispute in a free market context. But there are limits to what is rational, and I suspect there will be a significant percentage who will feel the workshop to be worth it merely because they paid a grand to be there. This "prestige" factor, after all, is one of the main components of a premium pricing plan.
You're mentioning a piece of advice that changes your product, but even just having someone like the 37signals team say "sounds like a good idea", "looks good" can be enough for someone to keep going.
I'm sure a 3h consultancy with a good copywriter will cost you more than $100 too. This isn't a day-job where it's ok to be paid $33/h. Professional freelance copywriters make (or should make) at least $100/h, if not more.