You are quite an optimist.  If you have any sort of serious charitable program of your own now, you would have to do extraordinarily well to affect your tax status. 

You can probably avoid unrelated business income tax (“UBIT”) issues by linking to and gaining commissions only on sale of products that, if you sold them directly, would be considered program related income from program services.  If you are an organization promoting reading with kids, for example, linking to and selling kids books would presumably not be considered unrelated business income.  To the extent you might sell some other unrelated books, you could pay the UBIT tax on commissions (not sales) over your $1000 deduction.  (See Ready Reference Page: “Nonprofits Often Worry About UBIT”)

If you are a “donative” public charity described in section 170(b)(1)(a)(vi) and receiving most of your support from gifts, grants and contributions (See Ready Reference Page: “Calculating Public Support”), you won’t get reclassified as a 509(a)(2) “commercial” charity until your program service revenue exceeds about 75%-80% of your total revenue.  If you were reclassified, or if you are already classified as a commercial charity, only 1% of the retailer’s commissions on sales each year would be counted in the numerator of the public support fraction, but the sales would have to be a huge percentage of your revenue to jeopardize your public charity qualification.

You are not likely to lose your exemption for private benefit to the retailer because it has thousands of other affiliates doing the same thing and you will not be adding more than a pittance to its profit.  You won’t jeopardize your exemption by selling related materials in the program and you can regulate your unrelated business activity by controlling the products you promote on your website.  You are not likely to lose your exemption for “too much” unrelated business activity because you can avoid spending a whole lot of time operating the unrelated business. 

You would probably have to sell more than $200,000 in products in a year (since most product categories have commissions of 5% or less) to generate $10,000 in revenue to your organization.  If you sell kids books averaging $37 each, that would require you to sell more than 5400 books a year, or about 15 books each and every day during the year (including the Fourth of July, Thanksgiving, and Christmas).  If you are counting clicks, how many visits does your website get each day, what percentage of your daily traffic would have to click off to the retailer’s site, and what percentage of those who look would have to actually buy a product to reach that level of sales? 

Even if you sold $200,000 in products to generate $10,000, what percentage of your current budget would that be?  What would you have to sell to make any significant difference in your budget?  Basically, I wouldn’t be worried about tax consequences of joining this program at this point.

It is good to be optimistic and it makes sense to give it a try if you can fit it into your program easily.  Just be realistic in your expectations.