"Why" is a bit tough. I can give a modern interpretation but it seems circular to me. Second inversion chords usually act as dissonances; bare fourths seem to imply second inversion chords, etc. The problem is that the fourth was something of a dissonance before the second inversion was common.
I have two references that should help. "The Evolution of the Six-Four Chord" by Glen Haydon. He tracks various uses of second inversion chords from the 1100s on. "A History of 'Consonance' and 'Dissonance' by James Tenny.
In the latter, the first chapter has some pre-1100s stuff with a fourth as a consonance. The second chapter has some discussion with the fourth being ambivalent by at least 1300.
Somewhere between simple organum at the fourth (C-F-C type) and organum with scale-like beginnings (C-C-C, C-D-C, C-E-C, C-F-C)...and three-part counterpoint, the bare fourth or fourth against the bass was treated as a dissonance.
These books (and other sources) do point out that physics "rules" do have a fourth as a consonance by looking at its sine wave overtones (Helmholz inter alia). Likewise, auditory tests show similar things. However, composers continue to treat bare fourths and six-four chords as dissonance.
A big point is that dissonance is "what composers treat as requiring harmonic movement" and consonance is "what composers treat as not requiring movement." It seems to work but It also seems to be mostly a cultural convention.