Imagine you have a bad guy in your neighborhood who keeps doing bad things, like stealing from your friends and hurting them. Your parents and other grown-ups decide that they have to stop this guy from doing more bad things so they make a plan to catch him and put him in jail.
Now let's imagine this bad guy has some friends who also did some bad things before, but they stopped a long time ago and now they behave well. However, just because they were once friends with the bad guy, your parents and grown-ups decide to treat them like they are still a threat and go after them as well.
This is similar to what some people criticize about the war on terrorism. The wars this past decade were meant to stop terrorists who were hurting lots of people, and this is a good thing. But some people think that the grown-ups went too far and also decided to go after people who weren't really a threat anymore, just because they were once friends with the bad guys. This made life harder for lots of innocent people and created more bad feelings between different groups of people. Some people say that a better way to stop bad guys is to work more with the good people in different countries, rather than just trying to find and fight the bad guys.