You're probably right that the increase is insignificant relatively, which is why the author left out the basis for the statistic and just cited the percentage.
Then there's also the fact that sensitivity toward hate crimes toward Muslims probably increased and many crimes involving Muslim victims may have been classified as a hate crime today, whereas previously it may have not been.
However, given the civil rights record in Muslim dominated countries, it should always be noted in any article about hate crimes involving Muslim victims in the United States, that Muslim terrorists commit hate crimes against non-Muslim civilians on a daily basis throughout the world without there being any repercussions for the perpetrators, and often state sponsored hate crimes in those nations is recognized by parades and celebrations.
As a demographic, Muslims have a long way to go before they can fully rehabilitate their public image, and just being model citizens is NOT sufficient. If Muslims want to fix their public image, they have to start by being the first in line to openly and rigorously reject Extremist and violent Islam. Until they do this as a group, merely pretending to civil activism isn't going to do much.
If they want to fix their public image, they are going to have to write a new koran, and invent a prophet who wasn't a mass murdering, baby raping pedophile, thief, and rapist.