The media has a tendency to portray women as sexual objects. If you pay attention to advertising you will notice that usually women are objectified. They are usually wearing skimpy clothing or made up to look like an animal or an object. This rarely happens with men in advertising. Usuallly men are dressed in nice suits or nice clothing, men should be handsome and women sexy. Granted this is slowly changing and now it's become more common to see men without shirts in advertising, and even a little male on male action (look at the ambercombie catalog). However now even the Ambercrombie catalog is considered "controverisal" because it does use half naked men sitting very close to each other.
The point of this is, the reason why seeing two women together isn't as uncomfortable as two men together is because the women aren't protrayed as "lesbians" but rather sexual objects which we are used to. It's sexy, not gay. Since we aren't used to seeing men in that way two men together automatically comes off as being gay. When in reality it isn't really any different, it just has to do with being used to seeing certain images.