Sometimes the good words of people that are not your direct family aren’t enough. And letters don’t have the same impact as your family telling you the same in front of you. Just remember the end of Parental Glideance. That was probably the first time she experienced what it is to be supported by a father and mother (even if they’re not). And it also explains why she was so mad at Rainbow when she saw how Dash treated her parents.

Honestly? Her parents barely seemed to give any thought to how Scootaloo would feel about them suddenly swooping in and dragging her off to the middle of nowhere. I’m inclined to believe that even if they want what’s best for their daughter, they’re completely clueless about what that actually is.

@FanOfMostEverything  

Assuming it’s the truth. It could easily be the hyperbolic comment of an angry, quasi-teenage individual who is angry at someone and looking to make a point. I mean, as IceKitsune pointed out, there are plenty of others around who could have offered encouragement, and likely did tell her how good she was at stuff. Counting strictly the parents who hardly ever get a chance to see her, however, doesn’t give much opportunity for those kind of comments.
 
But more to the point, consider the context of her home situation, and the situation she made that comment in. Scootaloo clearly loves her parents very much (her excitement over their return demonstrates that clearly), but is also proud of what they do, and doesn’t begrudge them being away from them because she considers their job extremely important. And then in “Parental Glideance”, one of her biggest heroes, Rainbow Dash, reveals that not only does she not want her parents around, she deliberately avoids having anything to do with them because she’s tired of how proud they are of her all the time. To someone like Scootaloo, that has to be quite the moment of emotional whiplash, and I’m not surprised it would result in that kind of statement.

@MadVillain  
I think its more that she was referring to just her biological parents with that line. Or else you would have to attribute that line to Lofty and Holiday, The Cakes, Rarity and Rainbow Dash at the very least. The last three just don’t seem like the type to not encourage her especially Rainbow.

Maybe Scootaloo lied?

@Background Pony Number 17  
I really don’t think that not telling your kid they would be the best at anything honestly reaches the level of neglect. It’s kind of shitty parenting sure, but I would say that Scootaloo’s Parents gallivanting off around the world; while leaving their kid at home to be raised by the town, and two aunts who come by every once in a while is actual neglect.
 
Lofty and Holiday not moving to Ponyville sooner is the actual neglect on their part. It was the one thing I was scratching my head at in the episode.

“Nopony ever told me I’d be the best at anything” does not have a lot of charitable interpretations.

OP hits the nail on the head here. There’s no sensible way to interpret Scootaloo’s character development in the show without concluding that her parents (including her aunts) were neglecting her.

In regards to Lofty and Holiday it could be that since Dash’s issue was with her biological parents that Scootaloo was only talking about what her biological parents didn’t do.