Here is an article very clear explaining why a boycott of Israel is justified, despite Israel not being the only country doing bad things. I think the strongest argument though is that it could work. Israel wants to be part of the Western world and it's citizens have influence over their government. Most of the other countries worth boycotting are already officially boycotted or under sanctions and the people who would be hit by the boycott are not in any position to change things. This is why South Africa was the subject of a popular boycott but Cambodia was not.
Jonathon Cook writes another interesting article this time following up on the Israeli invasion of Lebanon, including evidence that Hizbollah were not launching rockets from town centres.