In To Kill a Mockingbird, was Boo Radley mad when his brother put cement into the tree? And why did his brother do it in the first place anyway?

First, I want to be clear that it was Nathan Radley, Boo's father, who put cement in the knot of the tree outside of the Radley home.  Although he claimed to Jem and Scout that this was because the tree was dying, Atticus confirmed that the tree was very much alive.  In reality, the reader is led to believe that Nathan cemented the tree because Boo was placing gifts for Jem and Scout (carved figures, pocket watch, etc.) in the tree knot and that Nathan wanted to discourage such interaction.

As we do not see or hear from Boo until chapters later, we have no definitive way of knowing Boo's reaction.  One has to assume, however, that Boo was frustrated and upset by the action, as it cut off his way of "communicating" with Jem and Scout and his connection to the outside world.