The thing is, you have only one bomb per level. Once you deploy it will initially destroy all the monkeys in its vicinity. However, there are secondary blasts every affected monkey makes, and those are the main thing here. Every affected monkey can potentially destroy others who come across it. So make sure the density is good at that point where you throw your first bomb.

At the end of each level, you'll see how many monkeys you have destroyed. But, let me tell you something, destroying them all is a really difficult thing to do, so go back and try to achieve that almost impossible goal. Keep throwing those bombs until there is no monkey left standing.