It’s also strange to me since more then once when discussing startup naming I’ve quoted this earlier article Paul wrote where he makes nearly the opposite argument: http://aux.messymatters.com/pgnames.html
I’d also say the proliferation of new TLD domains has made them more, not less acceptable for new companies, especially ones like .io and .ly that have come to be pretty closely associated with the startups in general. Like you say, in 2006 nearly everything still was .com so a non .com might have stood out more as a negative, and even then pg says he still had no problems with del.icio.us
Also the last section stood out for me as a contrast with the title of this one:
"Whatever name you choose, be careful. Names stick. You need a way to refer to things, and whatever you call something rapidly becomes its name."