I think what it really boils down to is:
The war on terror: The United States (and allies) are fighting this "war" on terrorists, in hopes that one day it will actually end terror attacks on innocent people. They're living the illusion that we may one day live in a world of peace, and want to do their part.
Protesting the war: Basically against the idea of the above cause. Many thousands of people believe that the war being fought in Afghanistan and Iraq serves a different purpose and is trying to fulfill a hidden agenda. People who are against the war are probably against losing their friends and loved ones for a cause they don't believe has been 100% justified to them. In other cases, I would imagine that people don't see how securing oil and other resources is instrumental in procuring peace in the world. There are conspiracy theorists out there that believe this war is a mask to fulfill an agenda the government has and just need a "reason" to get to Iraq/Afghanistan. It's common knowledge that The U.S. openly funded the Taliban in the 70's to fight The Soviet Union and Iran, in order to protect U.S. interests in the region. Yep... The U.S. helped train THE Osama Bin-Laden. It's also common knowledge that The U.S. helped empower Saddam Hussein as well. If you notice, it wasn't until these people decided to embark on their own agendas that the U.S. decided to step in and fix the issues they helped create by assisting these people in the first place. I'm not totally for this war either, but I by no means, support terrorism. It was an ignorant comment, to say the least, because it doesn't distinguish reasons for people being for/against the war.