The most common reason boys get bullied is really quite simple; sexism.
Whereas women fought for and won the right to freedom from constrictive gender expectations, men are still very much trapped in "the man box", or the rules to being a man. (note that I'm not saying feminism has been "won", only that now a woman won't be criticized for say, wearing pants, taking a job as doctor, or anything else considered to be traditionally "male").
When you ask someone what positive attributes make a man "a man", they'll give you examples like "caring for their family, working hard, understanding the needs of others, being kind" etc. You'll realize that these are things we usually attribute to being a good person, and apply just as easily to women as men.
When you ask someone to truthfully tell you what defines "masculinity", they'll tell you something along the lines of "aggressiveness, dominance, competition, strength, power, heterosexuality" etc. Essentially, all fairly negative and violent attributes. The main thing to keep in mind is that masculinity is most importantly defined by being not femininity and not homosexuality.
By this definition, masculinity is something that must constantly be reaffirmed and put on display for others, whether it's proven by playing sports, fighting, having sex with numerous women, drinking, or pointing out and criticizing feminine qualities in others. Bullying, particularly the physical kind, is a display of dominance and therefore masculinity. The bully is reaffirming his dominance and masculinity, usually by picking a male victim who fails to meet a certain "manly" criteria.
What's most interesting about sexism against men is that it's enforced most strongly by other men. Rarely (though not "never") will a woman criticize a man for breaking gender roles, but if a man steps outside the masculine criteria, you can bet his circle of male friends will step in immediately to call him a "queer, pussy, fag or homo" (note that the most common terms men use to insult each other are based either in femaleness or homosexuality).
Anyway, the bottom line is that even though women have freed themselves from constrictive gender identities, "masculinity" is still considered highly more valuable than "femininity". That's why the little girl who likes robots and hates dresses is applauded, but the little boy who has an Easy Bake oven and doesn't like roughhousing with other boys makes his parents worry and is bullied on the playground.
People often overlook men's issues because males are given so much privilege in our society that it's assumed they have no issues to begin with. However, the way in which we define "masculinity" in our culture not only severely restricts men, but also encourages negative attitudes towards anything that is not included in the definition, like homosexuality and femininity.
Disclaimer: My message is not that being a man or being "manly" is evil. It is also not my opinion that everyone who gets bullied is inherently "unmanly". My intention is to make people think about how they define masculinity, and how they treat people who don't conform to that definition.