No, I'd say all of the main characters are liked almost equally. If I had to guess which one's the most popular I would say Rainbow Dash, but that is extremely debatable.
Results of the "Save My" contests I've run here and the past almost uniformly support the notion that it's Fluttershy.
(everyone loves the Moe)
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The Legend of Snake: http://tinyurl.com/3cal86z
The LoS Instruction Manual: http://tinyurl.com/3jlax8h