DeVos, a billionaire businesswoman who was elected to the position after much debate in Congress, went to Bethune-Cookman University on Wednesday to give her first commencement speech before hundreds of graduates at the historically black institute of higher education.
"Some of you may not like it, but she's here, we're welcoming her and we're building new relationships", Jackson said.
Her confirmation as education secretary was particularly contentious even for President Donald Trump's cabinet, only going ahead when Vice President Mike Pence stepped in to cast the deciding vote in an equally divided Senate.
The president of the NAACP said the students do not support the secretary and her values, and believes the university made the wrong choice by letting her speak.
"As we have said repeatedly, be careful of the people you let in your place", Jackson said, seeming to acknowledge the criticism.
"The bottom line is Secretary DeVos doesn't share our community's values and continues to misunderstand the impact and legacy that historically black colleges and universities have played in public education and America", the group said in a written statement.
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"I'm a student, I'm about to be a junior at Bethune-Cookman", said Bobby Luke.
Student Jasmine Smith, who helped deliver petitions to university leadership, said she felt DeVos was an inappropriate choice for her school's spring commencement, simply because there's so little common ground between her and the students she'll be addressing.
DeVos later amended her comments in a series of tweets the next day, reflecting the importance of the institutions.
"We have not and will not seek to chill the free speech of our students and faculty, as we support the free exchange of alternative ideas in all academic efforts", a university statement said.
Yet it was also clear DeVos had anticipated this response, opening her speech with a call for understanding. At times her remarks were drowned out by hecklers. "While we may share differing points of view, my visit and dialogue with students leaves me encouraged and committed to supporting HBCUs". But within minutes of speaking, DeVos was booed furiously by graduates and attendees of the commencement ceremony. "Ultimately, school President Edison O. Jackson attempted to quiet down the crowd by telling them" If this behavior continues, your degrees will be mailed to you.
It comes as little surprise that DeVos, the most controversial Secretary of Education in recent memory, was met with jeers.