Er, dunno. I read the Time article and thought it was astonishingly badly written and worse researched. The bit that puzzled me the most was that I remembered interviews with Ms. Rowling where she loved the Narnia books (it was a few seconds of Googling to find a 1998 Telegraph interview where she says, "Even now, if I was in a room with one of the Narnia books I would pick it up like a shot and re-read it.") as opposed to the Time version of 'Rowling has never finished The Lord of the Rings. She hasn't even read all of C.S. Lewis' Narnia novels, which her books get compared to a lot. There's something about Lewis' sentimentality about children that gets on her nerves.'
The version of the history of "fantasy" that the article's writer paints is utter bollocks, and I assume Terry decided that needed to be said. I didn't see it as a swipe at Ms Rowling, though, but as a swipe against lazy journalists -- but "Pratchett Anger At Shoddy Journalism" is a much less exciting headline than the one the BBC came up with.
(I remember when Terry said some very sensible and good-natured things about the power of fantasy at the Carnegie Medals (in this speech, read it first), the headlines were all along the lines of "Pratchett takes swipe at Rowling, Tolkien" [here's an example].)
Mostly what it makes me think of is the poem in Kingsley Amis and Robert Conquest's NEW MAPS OF HELL, which went, from memory,
"SF's no good!" they bellow till we're deaf.
"But this is good." "Well, then it's not SF."
And it's an odd double-standard that applies to all genre work as much as to SF. It's always been easier for journalists to go for the black and white simplicities of beginning with the assumption that the entire body of SF (or Fantasy, or Comics, or Horror, or whatever the area is under discussion) is and always has been fundamentally without merit -- which means that if you like someone's work, whether it's J.G. Ballard or Bill Gibson or Peter Straub or Alan Moore or Susanna Clarke or J.K. Rowling -- or Terry Pratchett -- it's easier simply to depict them as not being part of that subset. I'm not sure that writing letters to the Times will ever fix that, though.