Here's the part that I do understand: One of the first modifications that was patented was the ability to make seeds infertile so that farmers would have to buy new seed every year from the seed companies. Of course, the genetically modified (GM) plants have the ability to cross-pollinate with normal crops. So if a farmer using his own seed is unlucky enough to be near another farmer using the GM seed, and the GM plants cross-pollinate with his and he ends up with no usable seed for the next year, should that mean tough luck for the farmer?
The US Dept. of Agriculture gets a 5% royalty on sales based on this technology, so it's obvious what side they are going to be on.
Farmers need to be able to select seeds and cross-breed them to suit their local soil and weather. If the GM seeds end up cross-pollinating with regular plants, they can't do that any more.
There are obviously advantages to be able to make plants disease-resistant, but let's not fool ourselves that companies like Monsanto are doing this research just to make the world a better place. They'll make sure they get their money out of the deal, and if that means crops that do not produce any usable seeds - so the farmers must buy new seeds every year - that seems like a serious problem to me.