Being a part of a villainous organization may seem like a glamorous lifestyle, when you're not getting shot at or punched in the face by the good guys, but the average citizen doesn't see the glamour and fame, they simply see a group which threatens their way of life.
Who can blame people for being wary when you name your group the Legion of Doom or the Masters of Evil? Maybe it's time for a public relations makeover, so people won't know what to expect from your evil organization until it's too late:
The nefarious baddies who made io9's list of 10 Villains and Evil Organizations That Badly Need P.R. Makeovers have been too busy subjugating humanity, battling the forces of good and simply doing what they do best, to consider how their image is affecting their success as a whole.
They need to take a lesson from successful villains such as Richard Nixon, Walter White and the Stay-Puft Marshmallow Man- paint a pretty picture of yourself to the public, and don't let them see the real you until you've sunk your claws in deep enough to leave a mark!