What does Scout mean when she says "everything would come out all right" in To Kill a Mockingbird?

When Scout listens to her father during the Tom Robinson trial, she feels like everything is going to be okay. 

Scout has never been to a trial.  With all of the buildup that this one has had, she does not know what to expect.  The events leading up to it have been very dramatic.  The trial itself could hardly compare. 

First, everyone in town seemed opposed to Atticus defending Tom Robinson, the African-American man accused of raping a white woman.  Then, a group of white men tried to lynch his client.  Atticus was able to talk them down.  These events themselves were very frightening and stressful. 

Once the trial starts, Scout listens to Atticus and feels better about everything.

So far, things were utterly dull: nobody had thundered, there were no arguments between opposing counsel, there was no drama; a grave disappointment to all present, it seemed. Atticus was proceeding amiably, as if he were involved in a title dispute. With his infinite capacity for calming turbulent seas, he could make a rape case as dry as a sermon. (Ch. 17)

Scout feels safer with Atticus's calm approach to the trial.  After all of the chaos leading up to the trial, she starts to feel better once the trial starts and it is actually pretty boring.  Atticus always makes her feel safe, just as he made Tom Robinson feel safe when the lynch mob tried to attack him.

Things are not all right, however.  The trial may not be what Scout expected, but it is not dull.  Tom Robinson's freedom is at stake.  Atticus takes the case very seriously.  It is also very difficult for both Jem and Dill, who are older and understand what is going on better than Scout.  Dill is horrified at the racism Mr. Gilmer shows to Tom Robinson.  Jem is convinced that the verdict will be innocent, and shattered when it is not.