In activists' defense, a lot of industry support of all kinds of science has led to some pretty perverse incentives and results over the years. It would be far from unprecedented for explicit or implicit bias to be at work when one's paycheck is dependent on a certain result.
That said, I think part of the problem with the GMO "debate" is that GMO is like cancer in that it's not really a thing, but rather many things that all fall into some broadly defined category. I wish that there would be an anti-Roundup ready crop movement, and that this splinter group could wield more power than being against GMOs generally. There's not a lot of similarity, IMO, between Roundup ready crops and, say, a drought resistant yucca, but they're both "GMO" in the simplest terms. Unfortunately, this distinction isn't really made very often, and it leads to people being fearful. A scientist who even has the appearance of being connected to Monsanto isn't qualified to speak in a public outreach capacity on the topic of the safety of Roundup ready crops. Period. Nature Biotech being upset by this is disingenuous at best.
On the other hand, activist groups are certainly populated by lots of people who aren't very well educated on the topics against which they're advocating. However, these are the members of the groups who are most reachable. The ones who aren't are the very educated hard liners. Talk to a really hardcore global warming denier and (s)he is likely to know all the most recent studies. I had the opportunity to give a talk at a conference at Oxford last July to a group of animal rights activists about the work I do in therapeutic development for brain diseases, which necessitates the use of rodents as a disease model. I was called everything from a Nazi to a child molester, but I'm still glad I went. Despite these insults, I talked with quite a few genuinely interested (and interesting) people with whom I had very insightful conversations about the ethics of animal research.
The bad apples are an easy lot to cast aside as "crazy" or "anti-science", but it's never that simple. Protest movements often have a point, and there's viable signal if you're willing to wade through the noise. Dismissing the whole anti-GMO movement as anti-science is a sure way to guarantee that they will double down on their efforts. "Engaging" doesn't mean lecturing people about why they're wrong. It means listening to concerns as much as informing about what we know. One lesson that is clear from hundreds of years of science history is that there's a lot more that we don't know that what we do. Scientists forget this as much as anyone.