There are several times that Jem chooses to join Atticus despite discouragement or even direct orders to the contrary. Why does he disobey?in To...

To Kill a Mockingbird is just as much
a coming-of-age story for Jem as it is for Scout.  In the instances that Atticus tells
Jem to either "take your sister home," or do something other than what he is doing and
Jem disobeys, a couple of things are going on.

First, Jem
is asserting a sense of independence.  He wants to make his own decisions.  In some
cases (such as the night of the mob and later the courthouse scene) he does it fully
knowing Atticus will see his defiance.  Other times (the "Boo Radley Game" for instance)
he goes against Atticus' directions and hopes Atticus will not find
out.

In addition to asserting his independence, Jem is also
discovering what his role as man in the house is.  He is pushing boundaries with his
father because, as the oldest and the only son, he has an innate desire to feel a sense
of control.  There is a point in every boy's life that he must butt heads with his own
father in order to establish himself as a man.  He no longer wishes to be treated the
same way as Scout is treated (who Jem sees as a "child" and a
girl).

I would not actually consider Jem's disobedience a
negative quality.  In fact, I think this shows that Jem is not only very normal, but
that Atticus is a great father.  Jem often wants to be near his father because he
respects and reveres him so much.  His disobedience often comes in the form of wanting
to be places where Atticus is, rather than the opposite.  What a great testimony to the
role modeling Atticus has already provided.  His children are not growing up and
rebelliously attempting to leave home, rather, they simply want to be as included in
family affairs as possible.