The first big issue is related to quality, where Netflix users are saying that the Windows Media-based player is delivering much better quality video, up to the full quality Netflix currently provides. The Silverlight based player, on the other hand, does not. The second big issue is that the “opt-in” doesn't provide an “opt-out” down the road; once you've opted in to the Silverlight player, you are forced to use it permanently on any machine you stream with. The deceit came in to play after some people felt they were coerced or tricked into opting in. The final issue stems from Netflix apparently ignoring their customers – telling them essentially to just deal with the issues.
That's not to say Silverlight doesn't have any advantages. It does allow the content to be brought to other platforms, such as Intel-based Macs, which do not have Windows Media player. But are they making the right choice in preventing users from backtracking, even though it is beta software?