It is true that more than half of respondees reported that they never saw a violation.

However, the 44.6% was the category of "respondents reported knowledge of Honor Code violations that they chose not to report," and the 0.4% was the category of "had reported a peer for an Honor Code violation."

Everybody who saw a violation was in one of those two categories (did report or didn't report), so we can compare them to see what percent of people who saw honor code violations did, and the answer is that >99% of them failed to uphold their pledge.