Okay, here they claim that he criticized Lincoln’s decision to ‘invade the South’.
“One victim of Lincoln’s suppression of Northern newspapers was Francis Key Howard of Baltimore, the grandson of Francis Scott Key. Howard was imprisoned in Fort McHenry, the very spot where his grandfather composed “The Star Spangled Banner,” after the newspaper he edited criticized Lincoln’s decision to invade the South without the consent of Congress...”
http://www.321gold.com/editorials/mathid/mathid081308.html
Slightly different claim in this article.
“Howard wrote an editorial criticizing the Lincoln administration’s imprisonment of the city and state officials from Baltimore and Maryland without due process, and soon found himself joining them at Fort McHenry.”
http://www.thecivilwaromnibus.com/articles/94