The outsiders:
why does johnny start to shout and cry at the church?

  Because of his and Ponyboys unfortunate situation and destiny

Explanation:

This scene is happening in Chapter 5. Ponyboy and Johhny are boys who are committed to many crimes, they are young and they feel overwhelmed because of everything. In this chapter, they are waking up in the church that is abandoned and when Johnny returns from the store, they are starting to cut and die their hair. Whenever they think or remember about their situation they are starting to cry. They are also deciding that they will cry no more.