Those QBs you mentioned are the notable exceptions to the rule
If you look at stats of starting NFL QB height, you'll see that heights above 6'3" are the norm, with a surprising number at 6'5" and 6'6"
Labeling Wilson as small stems from a handful of things, in my opinion, including:
Youthful Appearance. Wilson looks like he just walked out of the DMV with his learner's permit
Slender Build. Wilson doesn't have a lot of bulk or definition in his shoulders/arms. Combine that with a flak jacket (which makes his torso appear disproportionately large and his arms disproportionately small), and you have the impression of a somewhat soft, small guy
Taller-than-usual Offensive Line. This year's OL was unusually tall (quite a few guys were over 6'5") and that makes Wilson look smaller by comparision. This is a genuine concern, because BYU's average 2020 OL height (though not weight) was comparable to many NFL teams - so if he looked small at BYU, he's probably going to look small in the NFL, too
That said, if Wilson fails in the NFL I doubt that it will be because of height. My concerns about Wilson center on his tendency to play hero-ball, his difficulty handling pressure, and his difficulty making accurate pre- and post-snap reads against complex defensive schemes. In my opinion, even though he's on the low end, he's tall enough - and he's mobile enough that he can reset the pocket in order to open additional passing lanes/sight lines, if necessary.