It's only been in the last 30 years we've been able to precisely modify our food with the traits we desire and limit the unintended consequences of random mutagenesis (which, by the way, we can sequence the entire genome of these transgenic plants to make sure we put the gene in the correct place). A common way to develop new traits in plants, that's been used for nearly 100 years, is to bombard seeds with X-rays and see what new traits develop. Of course, that's going to affect the entire plant genome instead of one or two traits we wish to alter or add (which can be done with genetic engineering). Did you know that the plants created through X-ray mutagenesis don't have the same regulatory hurdles that genetically modified plants do? And to top it off, it's not like "naturally" developed plants are inherently safer, take for example the poison potato:
http://boingboing.net/2013/03/25/the-case-of-the-poison-potato.html
The whole 'we don't know if it's safe' is the precautionary principle taken way too far and ignores all the science in this realm.