Many just intonation chords (where ratios are actually integers, not approximations of them) will sound out of tune to most people.
But the whole point of 12-TET is it is a close approximation of those just intervals while still allowing multiple keys to be played without retuning the instrument. If the close mathematical approximation didn't exist, there would be no reason to tune your instruments with a logarithmic recurrence relation.
Both statements are true. We have a strong tendency for integer ratios in harmony, and just intonation often sounds out of tune.
Integer ratios are the base upon which harmony is built. Temperament is a subtle modification that sounds very close to integer ratios, but allows more complex harmonic structures where dissonance is evenly spread out across all the relationships between tones.