I'm all for GM crops, but they do have problems- most notably cross-contamination with the natural breed of the crop. This will tend to reduce biodiversity and eventually the availibility of new genes to splice into the GM crop to enhance yield, disease resistance, etc. I know this from A-level biology, so I haven't got a complete picture by a long way, but my own view is that GM is fine- as long as it's done responsibly. All too often, it isn't.
Then there's the fact that the agrochemical companies to make a fortune off what is supposed to be helping others. I'm fairly left-wing politically, so I'm not really comfortable with that, but I guess it's a necessary evil.