The question is whether this is a fad or not. Companies always try new marketing tricks. The type of marketing that stays is the marketing that benefits the company.
This type of group buying is relatively new and lots of companies (small and large) are testing it out. They're willing to chance making a bad decision to see whether it works or not. The question isn't whether Groupon is getting a decent cut, but whether companies are going to see this as a long term part of their business in the same way that other marketing techniques are. Businesses might find that they try it out, lose money, don't get repeat business, and it becomes another thing that no one uses in a couple years.
Groupon's business is that it has a mailing list (basically) of people looking for deals. That's the service they're offering businesses. At what point do deals of 50% off or more need such publicity? So, even if they become the 500lb gorilla and group-deal marketing isn't a fad, how likely is it going to matter? I'm not saying that it doesn't matter, but truly great deals tend to be spread (I'm remembering an Old Navy one that half my friends posted on Facebook).
Beyond that, there's a danger in marketing to people specifically looking for deals - and specifically people looking for deals that don't require much hunting. Companies spend a lot on price discrimination (getting people who will pay more for a product to do so). Companies use coupons that people willing to pay more will ignore or forget about, they sell different editions of products to get the back of your head saying, "I can't tell a difference, but am I going to be disappointed if I buy the cheaper one?", etc. If Groupon becomes so popular, there is also the risk that the deals will become easy to the point that you aren't getting extra marginal business to people who might not buy your product, but rather lowering your average price since so many people are on it. In fact, using a less-known deal site might be beneficial since it could grab the people who really wouldn't pay full price while flying under the radar of those who are just casual deal people.
The worst thing might be if the government decides that Groupon is selling gift certificates. Gift certificates are regulated including things like expiry dates. Right now, there's the possibility for me to spend $20 for $40 of goods and forget to redeem it within the (usually) short redemption period. That might change as Groupon gets bigger or one Groupon user decides to sue over the expired "gift certificate" and a judge sides with them. In fact, at least in Massachusetts, Groupon the gift certificate law would seem to apply since it includes merchandise credits and "and any other medium that evidences the giving of consideration in exchange for the right to redeem it for goods, food, services, credit or money." I haven't looked over Groupon's filings, but that seems like it would impact on their business - either by taking more money from them or the business depending on who keeps the revenue from non-redeemed cards. And even if it's the business, that means a change in how willing businesses are to sign up. I'm sure businesses are keeping track of how many sold to how many redeemed.
I'm not saying that Groupon is terrible or won't become valuable. However, there are pitfalls. "Group buying" might be a fad. Businesses might not find it in their interest to give Groupon half of the revenue or might find these lazy deal-hunters not in their interest. Larger size could become a hindrance as the larger they get, the more it will affect average sales price rather than just marginal sales price. And the government or courts could affect their business model. New things come with risk, but when the founders start taking a lot of the cash they receive as investment for themselves (rather than for the business), it's a bad sign for me. They're signaling that they see their business as risky enough that they want to make sure they're covered if and when it goes belly up. They aren't holding their wealth in Groupon stock; they're holding it elsewhere.