I've been using Checkout since about January 2007 to sell digital resources through my site gmathacks.com. In that time, I've had thousands of purchases through Checkout with gross sales well over $100k.
Having had problems with PayPal before (not with this business, but a previous one), I was careful from the outset -- I generally err on the side of refunding people, I follow Checkout's procedure (click the "shipped" button, even though it's a digital product, etc.) to a "t," and I do the best I can with customer service in general.
My experience has, quite simply, been great. Checkout's algorithm seems to reject some purchasers more readily than other systems do (often, I think, because their IP doesn't match the country in their credit card address), which is better than a recent experience of mine through PayPal, when a $200 purchase was reversed weeks later because of a fraud concern. (Which turned out to be false.)
All the while, the fees charged have been way cheaper than PayPal's. (This, unfortunately, is changing. Depending on your monthly sales, Checkout fees are going up as much as 40% in the next month or two.)
I will say that little has happened to turn Checkout against me -- in 2+ years, my chargeback rate is just a shade over 0.1%. And as noted, I'm aware of some of the risks, so I've trod carefully.
All of this certainly isn't a defense for Checkout's (non-existent?) customer service and apparently faulty algorithms. But...while I'm glad to be aware of situations like this, I'll continue to happily use Checkout and recommend to others that they do the same.