1. They may have taken advantage of special tax credits offered by the government for activities that it was deemed to be in the best interest of society at large.
2. Ebay UK may have carry-forward losses from a previous year that lowered their tax.
3. These "sales" may just be gross revenue, completely ignoring the issue of COGS, which means gross income might only be $50m or something much lower. I know the article cited Ebay's global profit margin as being 23%, but is that on gross revenue or gross income? That seems high to be on gross revenue...
4. This revenue may have been earned by subsidiaries owned by Ebay UK, but the money was never brought into the UK and has been reinvested into those subsidiaries. For example, Ebay UK owns Ebay Monaco, where there are no corp taxes. Ebay Monaco does $10m in profit. If they sent that money back to Ebay UK, they'd owe UK taxes on it. Instead, they reinvest it into hiring more staff and expanding the Monaco office. If and when the money goes back to the parent entity, it'll be taxed then.
Getting upset about corporate tax law based on newspaper articles is a fool's errand.
EDIT: More details:
http://www.forbes.com/sites/timworstall/2012/10/21/ebay-is-n...
Looks like they're just taking advantage of EU law to have payments from consumers go to a subsidiary in a lower tax jurisdiction. How is this different from running your company in Texas instead of New York for lower state taxes?