Our lives can become dominated by fear affecting our decision making (rather than relying on faith).
Jesus encourages to take courage because He is with us; God is omnipresent. He has perfect power, wisdom, and love.
We can be afraid of nature (like a storm), and afraid of Jesus' actions (walking on water). Through their fear they learn something about Jesus. He shows us that He has the power of the curator over the creation (is the divine son of God).
Humans are compared to sheep in the Bible. Courage is the ability to do something that you're frightened of. Jesus showed courage when facing death on the cross. The Holy Spirit can reproduce this courage in our lives - we need to pray for this.
We all struggle with fear, but we know that God is always working in our lives for our good.