No, they are not unfounded. After reading these results, I think they went into a lot more effort in clarifying their results this time around. I do not feel ashamed to share institutions with one of them now.
I will say though that I'd believe a lot of the respondents come from Equestria Daily, because that's where I saw most of the recruitment done. I don't know if they went into other sites with significant numbers of broneis (bringing that spelling back now), many of which do not visit Equestria Daily (e.g., Ponibooru, FIMchan, /mlp/). I know a lot of news is stuff I have to present here, because at one point, most of you didn't frequent Equestria Daily very often. If many other smaller subcommunities of broneis are the same way, then their sample probably wasn't representative of the brony community on the whole. I know that many users on Ponibooru hate EqD and their commenters, because they see them as being overly concerned with morals and have already made a point to remove anonymous posting to prevent/reduce trolling.
Given that reason for disliking EqD (which is tied to how nice we are as a community,) I'd say that you'd have entirely different results from Ponibooru, FIMchan, and paheal, some dA's, some tumblr circles, and maybe /mlp/ (I haven't been there recently to know how they feel about various matters of morality, kindness, or anything.)
So I'd say that would be some evidence that this particular portion of bronydom (to "steal" a term from opspe who stole from me first but PATENTS AND SH!T) is nicer than non-bronies. But even in that, I'm sure subjectively "nice" can be twisted by using objective measurements to yield insignificant results.