The important thing to remember is that humanity is at odds with God and, due to the choices made by human beings, they have created for themselves a world which is painful to live in.
"Although they claimed to be wise, they became fools and exchanged the glory for the immortal God for images made to look like mortal man and birds and animals and reptiles. Therefore God gave them over to the sinful desires of their hearts..." Romans 1:22-24a
God has immeasurable patience by human standards, but there still comes a point where He decides that enough is enough. The fact is that God is just and cannot tolerate sin, and He does punish it, but not indiscriminately. But if we see sinful attitudes and lifestyles being promoted and little being done about them, we can understand that God does, at times, give us what we want - and if that happens to be slavery to sinful desires, we can expect that consequences that accompany that.
"We know that the whole creation has been groaning as in the pains of childbirth right up to the present time." - Romans 8:22
Natural disasters can certainly be seen as a part of this groaning, and elsewhere that groaning is explained as being in anticipation of the adoption of the children of God - all humanity. We can infer that creation itself is in a fallen state due to the corruption which humanity invited upon the world. The violence of creations towards humanity is a symptom of that and, while certainly a tool at the Lord's disposal, it is still a consequence of our decisions which He has allowed us to make.
That is, of course, until Christ returns and reclaims Humans, Heaven and Earth as his own once again.