Justin - it's true of any complex system, not just GM. The main problem is the GMO has been reduced to a few talking points on either side (mostly the negative side but by no means entirely) which makes the discussion, well, wrong :-)
The herbicide is but one of so many GMO improvements (if we restrict it to actual gene manipulation), but if we look at breeding, splicing, and other previous techniques, as well as evolution, then the examples are in the millions.
In a considered cycle of crop rotation and pest management, the GMO crops reduce the amount of herbicides needed. If people don't follow the recommended protocols, then resistance can develop and then you have evolved yourself out of an advantage. It's like over prescription of antibiotics or prescription of them for people who don't have a bacterial infection but just want "something" so the doctor gives it to them. The issue is far more known and aware now, but like anything, when you stop following the instructions, things can go wrong.
Perhaps the biggest irony in the whole debate is that "organic" (and, really, everything we eat is organic by definition - the term has been co-opted for marketing purposes) usually requires more pesticides and herbicides - they're just considered "natural" ones.