Well the show wasn't that consistent in her portrayal anyway, they had one episode where she dealt with her shyness, and then another in the same season.
Would you care to be more specific?
Yeah, sorry. in Putting your Hoof down, Fluttershy overcame her shyness by becoming overly assertive and being a dick to everyone, at the end of the episode she was supposed to have learned that she can be assertive without being overtly agressive. then in Hurricane Fluttershy, she goes right back to being really shy.
I think Fluttershy's shyness in Hurricane Fluttershy was more of a "I can't do it." kind of shyness, and not quite the same "If that's okay with you." shyness I constantly see in fan portrayals. Also, she's been a lot more confident in herself after getting over her self-doubt in flying.
I think that the episodes dealt with a different kind of shyness, and especially a shyness unlike her shyness in season 1. Each time she's dealt with things holding her back though, she's come out stronger.
Regardless, her shyness sure isn't the "shyness taken to 11" that a lot of fan memes portray.
