There is most certainly a gap in raw power between unicorns and other nonmagical races, but not an insurmountable one.  As seen with the Hearth’s Warming play, the unicorns were once the group that would raise the sun and moon before Luna and Celestia, but they were still subject to the other races in that they cannot exist in a pure vaccuum, and need help to remain in power. 

As far as raw potential goes unicorns do have an advantage due to the flexible nature of canonically displayed magic, but an important thing to remember is that those that can use magic well use it only with YEARS of practice and study.  Earth ponies don’t have this hurdle and can use that time to spread influence, gather followers and become a threat through wiles and power.  Pegasi can use this time to manipulate the weather in their favor, and have a more militaristic history.

It’s not hard to imagine an Earth pony or Pegasus villain, it’s just a matter of figuring out how they come into power or pose a threat.  Earth ponies are social and physically powerful with a greater ability to manipulate their landscape and so can more effectively limit food supplies, control land routes and generally physically bully other races, but they must act with tact and wit rather than sheer brute force.  Pegasi can alter the weather as their needs dictate, be that to attack or to hold siege over an area, and can potentially do it with small, directed numbers or even with a single individual (talents allowing).

It’s not a matter of unicorns being more powerful and being villains, it’s a matter of having the unicorns elasticity in ability making it simpler to portray them as villains.  There’s less to explain when you have the excuse of “I have magic” up front, but there’s still the aspect of time with the study required, as Starlight mentions.  It’s all a matter of how things are explained for the audience and how things are presented.  All races are viable as antagonists, unicorns are just easier to set up.