Given the limited # of characters it is, as even you might appreciate, impossible to "TELL THE WHOLE STORY."

In brief, Lincoln had an array of threats, from secessionists in the Border States to abolitionists who felt that he wasn't doing enough, to numerous politicians and journalists who were highly critical of his choices to lead the Northern Armies.  Burnside, Pope, McClellan, Hooker, Rosecrans gave plenty of ammunition to those who believed that Lincoln was unfit to be president.

When these journalists made too many overtures about making peace with the South, or gave up information which Lincoln thought could benefit the South, or found too much fault after disasters such as Fredericksburg or Chancellorsville, Lincoln had them jailed.  Estimates range from 2K - 15K.

It's important to note also that Lincoln was also a scofflaw regarding Habeus Corpus. Prior to 1863 only Congress could withhold it, but as the Merryman case proved, Lincoln again ignored the law for his own ends.