The fact that people don't know what a pocket square is is sad...but you may be right :)
Interview tie that's conservative but not corporate? - Page 2
That is not normally the reaction I get. Tasteful PS's just accentuate an outfit without standing out. If you go for some huge poof or octopus looking thing then I'd imagine you could get that reaction. An understated linen square or color accent normally comes across well, I think, and I have only received positive comments about this.
That's not to say that there are people quietly loathing your pocket squares. I'm sure you look great. Just as a general principle, do not use random comments made my others to judge the success of your outfit.
When dressing for a job interview, the tenth percentile of opinions on your dress is not the order statistic you want to aim for. You want your dress to be unobjectionable to all, so that they can focus on what makes you a great candidate (hint: it's not in your breast pocket). A great outfit is never going to win you an assistant professorship, but one that is perceived to be unnecessarily showy may support an impression of you as vain or arrogant, which can lose you the job.
Again, the chances of a white linen pocket square making any difference at all are pretty slim. It doesn't really matter one way or another. But when in any doubt at all, I'd suggest going without.
Thanks for all of the advice. Very helpful. I'll do some more asking around and try to get clearer details. I do think that I'm over-thinking things though—I was just talking to a friend who went through this last year and he told me that several places actually instructed him before the interview that he need not wear a suit at all!