Baxter and Vernon share a very strange and sometimes rocky relationship.
Initially they do not care for each other at all, with Baxter branding Vernon an idiot and Vernon considering Baxter a horrible fly creature. It is Vernon's report that brings all of New York to the realization that Baxter was the giant fly that terrorized New York, which complicated his job at Channel 6 at first and still results in some shunning and disgust from people around town.
Despite his dislike of Vernon, Baxter begins to feel that Vernon may actually have untapped potential and depth after realizing that even though Vernon is branded a weak coward by everyone else, he has been quite resilient in the face of so many terrible things happening to him and has always bounced back instead of having a nervous breakdown. The Turtles, naturally, find it difficult to believe that Vernon is anything other than shallow and self-centered.
When Vernon is taken over by a force from an alien crown, it is Baxter who insists on Vernon's ability to fight it and is able to get him to do so. Baxter is also there to listen and try to offer support when he and Vernon go through the frightening experience of having their spirits pulled out of their bodies and believing themselves to be dead.
Vernon's opinion of Baxter seems to be gradually changing; he is amazed that Baxter actually speaks to him in depth and doesn't just dismiss him like everyone else does. Baxter has uncovered several of Vernon's secrets and unearthed traces of goodness that no one believed existed. Perhaps someday, the unbelievable will happen and Vernon actually will begin to change for the better.
Since Vernon was apparently created to be a negatively static character, it's difficult to find any goodness in him and I was at first hesitant to even try. When I was writing Twin Beaks and started writing Baxter's first impressions of Vernon as a stronger person than anyone believes, I balked and tried to remove it. But I realized that it should remain regardless of the truth about Vernon, because Baxter's experiences of always being branded weak and worthless may have given him a more compassionate outlook now that he is sane and trying to live a decent life. And amazingly, I actually have found a few grains of goodness in Vernon as I've re-watched assorted episodes. These I bring into play in the stories. While much of Vernon's negative behavior can never be excused, I at least want to explain it better so that he feels like a more well-rounded person. And that combined with what goodness he has may help him start to develop in a way that is actually not out-of-character with what is shown in canon.