My Little Pony: Friendship is Magic - They're rare allright...

Most of those scenes are during the Great Dragon Migration where all the dragons in the world get together (to mate, that’s what most migrations end in) and we see maybe a few hundred. A few hundred in the whole world is not a lot, like the low end of endangered species levels of low. And outside of that they’ve seen three other dragons; one that was hatched and raised by ponies, so only two have been seen in the wild under normal circumstances. Compared to the pony population which based off of their medical and agricultural technology should be in the tens of millions at the least.
So yes they are 'rare.'

"Too rare and scary".

I think the "scary" factor may have something to do with the lack of information. They're rare outside the dragon realm, and when they come to Equestria, the ponies are too afraid of them; ergo, it still makes sense.