The raw data can be found at the FBI's web site, with tables for 2005 and 2006 here and here. The data show a much different story than that painted by the AP.
Yes, from 2005 to 2006 the total number of incidents increased from 7,163 to 7,722 -- a 7.8% increase. And yes, racial incidents continue to constitute a majority of incidents, 51.8%. But that's where any similarity to the truth, and the AP's account of it, ends.
Overall, racial incidents increased only 2.1%, and anti-black incidents increased even less, at 0.4%. So while the AP article speaks almost entirely of anti-black hate crimes, the growth of anti-black incidents rounds off to zero.
However, anti-white incidents increased 7.5%! In fact, there were 81 more racial incidents in 2006 than in 2005, but 62 of those were anti-white, while only 10 were anti-black. That's right, the bulk of the increase in racially-motivated hate crimes were anti-white.
The AP also fails to note that anti-religious incidents increased 19%, with anti-Jewish incidents accounting for two-thirds all anti-religious incidents, and increasing 14% from 2005 to 2006. One surprise might be that anti-Catholic incidents increased 31%. Another surprise: anti-heterosexual incidents went up 24%.