No one outside of FIFA and/or South Africa knew how horrible the vuvuzelas are until the massively televised Confederations Cup in the summer of 2009. Unfortunately, FIFA awarded South Africa the 2010 World Cup years before that. So, at the time FIFA made its decision, there was not yet a worldwide hatred of vuvuzelas. Further, maybe there was not even such a thing as a "vuvuzela" way back when South Africa was awarded the World Cup - I don't know how long vuvuzelas have been used at matches in South Africa.
I think what this all means is that FIFA is only moderately (instead of wholly) incompetent for not spending the last year since the Confederations Cup figuring out how to ban vuvuzelas without upsetting South Africans.
Worse though is the way that FIFA's president Joseph Blatter has handled the situation. His approach has basically been, "It's a South African tradition that we're not going to interfere with. How would you like it if we banned your own, unique traditions."
The better approach would have been to just simply admit that it is a problem that FIFA didn't and/or couldn't have anticipated, and that FIFA will do what it can going forward.