The most annoying difference is MP3's harshness in high frequencies, particularly cymbal sounds and esses in vocal tracks. And these flaws can be heard even on mediocre equipment if you're accustomed to listening for them. The frequency roll-off at the top and bottom can't completely be overcome with EQ as claimed in the article, because some information just plain isn't there. However, these annoyances are so minor there's no point worrying about them except when you're doing some critical listening in a quiet environment. If you strictly listen in noisy places, or the car, or while exercising, etc., there's no reason to care about FLAC.
With that said, I could have a FLAC file that's the same size as MP3, obtained through equally convenient means, without the sonic drawbacks, why not have that instead? It's a bit like saying you can have a steak for the price of a hamburger and choosing a hamburger anyway. That's dumb.