In my opinion the difference is that PDF is the lesser of two evils when it comes to PDF vs. Flash, whereas Flash is the lesser of two evils when it comes to Flash vs. WMV.
You haven't considered the difference in the formats. A key advantage of YouTube over WMV is that it loads instantly, makes streaming-while-it-downloads simple and transcodes into a quick-to-load low-bitrate version, which just completely doesn't apply to PDF - viewing PDFs using Scribd actually makes things slower and more clumsy /not/ faster or more accessible from my end. PDF is also a open format, a de facto standard and cross-platform compared to multiple codecs for video which can make life harder than necessary for viewers. Another key difference is that Scribd is used by the site as an unwanted front-end to content readily available elsewhere - compare this to YouTube which is often the exclusive host of their content and so there isn't a choice.
FWIW, when an alternate format is available for a YouTube link I often use them too as it makes life easier for managing windows or deciding to keep on the desktop knowing I won't need a net connection or have to buffer later. A recent example was John Resig's talk on the future of jQuery which was available as a download on Vimeo.