Why is GrapheneOS against GNU?

I'm not sure exactly. But I personally don't like GNU because I think they have been embedded in a form of wishful thinking for far too long. Expecting that developers and manufacturers willingly relinquish their rights to their copyright for the benefit of others, regardless if they want to or not. And expecting that end users only seek out those kinds of systems as well. In total, providing everyone with free reign with minimal regard to consequences. And pushing away those that simply want to try and make the things only a little better.

For an organization primarily devoted to ensuring that software remains open, accessible, and modifiable, they sure do seem to like to bend over backwards. Looking directly at GrapheneOS, my personal thought would be the fact the goals of GNU tend to conflict with the goals of security (the FSF has actively spoken against the concept of Tivoization, or systems that use free software but are locked down by hardware restrictions)

They're also horribly out of touch with the general public. And in some cases, simply too radical to be taken seriously. To name a few examples:

• They have very little understanding of the actual public or anyone else outside of the tech field. Their Gift Guide is an absolute joke, suggesting adapters and old ThinkPads as gifts. With their most appetizing gift (a Vikings D8 Desktop computer) is literally mentioned as being out of stock. Suggesting you instead give, once again, a ThinkPad with Free software. Their only reasons for not using an actively manufactured and relatively modern (as in 3 generations ago) computer that are because of "restrictions to users freedoms" and "spyware" without very much definition aside from a few links (they've got much more to say about the computer than they what they believe in).
• Their "preferred terminology", lists a bunch of jargon they don't like and their alternatives, making a lot of automatic presumptions of guilt. My personal favorite is "Internet of Stings". As if projects like Home Assistant aren't trying to improve the scene (though they're presumably ignored because they're also willing to connect with proprietary services)

TL;DR the GNU foundation is made up of a bunch of nerds who care more about messing with their computers than actually trying to do important things with them.