I think it is important to acknowledge the anger and why it occurs, more important than worrying if you should even feel it. You do feel it, and suppressing it will not help.
In a song of Asaph (Psalm 73), the Psalmist is basically angry at God. He doesn't understand why God has allowed wicked people to prosper. It looks to him as if the good people suffer and God is not doing anything about it. After expressing his anger and his ambivalence at expressing it, he meditates on the future promises from God, namely, to bring justice. This is inspired word, showing it is natural to have these feelings and not offensive to God.
In addition to mediating on the future, you can meditate on what has happened in the past (Biblical and personal) to understand how God acts and what qualities these display. There is a lot of misconception concerning justice and mercy from God, especially in the "old testament".
Also consider where problems or disappointments really come from. Are they truly from God? Does God fail to act or he is patient? Does God not act to prevent suffering because he is cruel, or does he allow us free will and the consequences of it? Does God not answer our prayers because he doesn't want to or can't or because he sees the long-term better than we do? Reconciliation with God means humbly acknowledging the need for his support and direction to live a happy life, but people insist otherwise, and he let's them have their way. Working through why you feel angry is a good first step to reconciling with anyone. This can help to redirect anger and come to view God as a support and guide that empowers you to deal with what angers you, not someone to be angry at.
