This is likely because as you've said, the number of hate crimes are low compared to the overall population, which is 6370. So statistically it tips the scale of the total percentage more easily.
This is the actual number of hate crimes by race:
Blacks: 1356 (21.3%)
Whites: 3299 (50.7%)
adjusted for population size:
Blacks: 802 (12.6%) -554
Whites: 3866 (60.7%) +567
https://ucr.fbi.gov/hate-crime/2017/...ages/offenders
So adjusted to actual population, it's an error margin of ±500. Now 500 could be significant, or it could not. But the fact is that 500 cases could change as much as 10%.
Your claim that "blacks are significantly more likely to commit hate crimes than whites" is simply not true.