Imagine if the JFK CTer/contrarians applied their usual standard of proof to this situation.
1) No one '"saw" Booth shoot Lincoln. They merely heard a gunshot and turned to see a man resembling Booth holding a smoking gun at Lincoln's head. That doesn't mean they saw him shoot Lincoln. It's possible Lincoln committed suicide, Booth picked up the gun, and realized it looked bad and made a run for it.
2) There is nothing incriminating about Booth being there since he "worked" in Ford's Theatre.
3) There is a chain of custody issue with the gun since different people claimed to have found it after the shooting.
4) There are no documents, photos, or prints that link Booth to that gun.
5) Why would Booth, who was wealthy, use such a weapon? Surely, he would have brought a better gun.
6) There are some witnesses among the crowd who were off in their description of Booth's appearance. They got some details about his manner of dress, weight, and age wrong. Therefore, we must entertain doubt that it was him.
7) Booth's diary and other written materials could have been forged since handwriting analysis is not a science.
There were powerful forces that wanted Lincoln dead during the Civil War.
9) Booth's motive can't be proven with certainty. The war was effectively over. So killing Lincoln was not going to accomplish anything at that point.
As a result, we can never conclude that Booth was guilty of the assassination. It is only our "assumption" or "opinion" based upon acceptance of the official story.