Maurice Eisenstein, a political scientist who teaches at Purdue-Calumet in Hammond, made the comments on Facebook in November, questioning why moderate Muslims were not criticizing Muslim attacks on Christians in Nigeria. He also made comments about the Prophet Mohammed, the Lafayette Journal and Courier reported.
Students on the campus held two days of protests, demanding Eisenstein's ouster.
Eisenstein Monday released a letter the Foundation for Individual Rights in Education sent last month to Thomas Keon, chancellor of Purdue-Calumet.
"Please do not let your students abuse the university's disciplinary process in order to interfere with the free personal expression and academic freedom of one of your own professors," Adam Kissel, vice president of programs at FIRE, wrote.