Her reluctance and shyness can easily get on ones nerves after a while, and I'll give you that one...
But think about kids who are watching the show that are really like that (albeit, to a lesser extent) and relate to her. I've suffered from social anxiety since elementary school, and literally, I'm more afraid of being judged, laughed at, and embarrassed than I am of death.
As exaggerated as that sounds, it's true.
When she was trying to help, but kept hearing other ponies laugh at her in her mind, I related to her so much at that moment. I have let fear of embarrassment or failure keep me from doing what I need to do so many times in my own life, and seeing her overcome that and make a huge difference in the end, despite her fear, it just really touched me.
And yes, she will go back to being shy and reluctant and scared as always. People don't always change because of one triumph, and I can confirm that personally. I'm in a performance group, and I always pull through, and the show goes great, but the next day I'm back to trembling and blushing and stuttering when a stranger speaks to me.
I think it's only realistic. I know it might be hard to relate to, and even annoying if you don't experience it yourself, but that's why there's a pony for every type of person. We can all relate to a pony, some more than others.
I think some ponies need to be a little exaggerated, and even sometimes annoying, because it balances out the other personalities beautifully, which I think really compliments the series as a whole.
tl;dr Fluttershy is shy for a reason, and I relate to her a lot.