I'm not sure because deals Netflix has with different studios can be a little weird. It's like they rush to get the first season of something on instant view but then they sometimes drag their feet on the later seasons. Some studios have been adapting quickly to the rise of internet based entertainment while others drag their feet. For example South Park usually has new episodes up on their website in a matter of hours but Warner Brothers seems dead set against instant streaming of their properties.
Check this thread...that was quick! http://www.tfw2005.com/boards/transformers-prime-discussion/725593-prime-season-2-netflix-streaming.html
Season 2 of TF: Prime is not up for streaming just yet. Please be patient. ...Beast Wars was all added at the same time. Season 3 is up there.