Board Thread:WARNING ALL USERS False Info\Spoilers/@comment-11489125-20130829192954/@comment-1587802-20130829215717

Pretty much what the people above have said.

If you want to know how it's been explained directly in the show, Peter first mentions it in 311, describing it to Derek as "that spark of power that makes you an Alpha, the power that provides you with those special gifts which Cora draws on when you heal her, the power that heightens your senses, your strength, the power that transforms your body. As an Alpha, you have that extra oomph, that spark, that intensifies the color of your eyes from a bright yellow into a seering red".

Basically, every Alpha is an alpha because they have the "alpha spark" which heightens your senses and your strength beyond that of a normal Beta werewolf, and that has the power to change your eye color to red.