Actually the first NYT reader was WPF.
Silverlight 2 (the latest stable version) and below is a web only technology, while Flex is both a web and offline technology, running on either AIR (for offline ability), or Flash Player (for online ability). Since this is not a web site, but an application, Silverlight doesn't even make any sense at all for this application. You can tout Silverlight all you want but this is just a fundamental misunderstanding of what Silverlight is. Microsoft Silverlight as a competitor to Adobe Flash Player. Not to Adobe AIR. At this time Microsoft has no [stable] product that competes with Adobe AIR.
Another interesting thing about Flex which is NOT POSSIBLE in Silverlight is the ability to leverge Adobe Flash (the productivity program), to create useful Flex assets.
Flash is a program where there is already a lot of expert knowledge available. This is HUGE. Adobe products have a virtual monopoly in the designer market, and Adobe products all interoperate with one another very well.