Because Jesus said it would happen, that's why. He did not say that people would hate Him because of those Christians over there. That is a common temptation: to assume it's those Christians over there whose bad witness is giving Jesus a black eye. Goodness knows I've succumbed to that temptation once or twice before.
And it's not to downplay the importance of a good witness. And generally our witness is best when we do the work of the Faith: love, charity, mercy, forgiveness, reconciliation, helping the widow and orphan, clothing the naked, feeding the hungry, visiting the prisoner, and doing all in the name of Jesus Christ.
Nonetheless, despite it all, Jesus assured us that the world would hate us because it hated Him first. While we can scoff at Church Militant, Michael Voris, or any particular expression of Christianity, we're also being fools if we think that it's their particular witness that is causing all this. Unless Jesus just had rocks in His head, there's a good chance that had Voris never been born, the same protesters would gladly hate Christ's and His Church on other grounds.
No. Thinking that if we just do it right then all will work and the world will convert and we'll do what nobody from the Apostles down through today could accomplish, is borderline hubris at best. It also seems to ignore a big part of the Apostolic teaching about the price we pay for following Christ.
This isn't to say we just throw our hands up and consign future generations of Christians to suffering we never had to endure. As beneficiaries of a free and democratic society, we are obliged to protect religious freedom and, indeed, all liberty for all people as long as we can.
It's just to remind us that when we see overt hatred of the Gospel, of God, of Christ, or of Christ's Church, we shouldn't immediately look around and wonder who is the cause. Dare I say, if we do that, there is a good chance that we need to look no farther than the nearest mirror to find out whose fault it is. Since we likely forget who it was that promised us hatred from the world to begin with.
If the world hates you, keep in mind that it hated me first. If you belonged to the world, it would love you as its own. As it is, you do not belong to the world, but I have chosen you out of the world. That is why the world hates you. Remember what I told you: 'A servant is not greater than his master.' If they persecuted me, they will persecute you also. If they obeyed my teaching, they will obey yours also. They will treat you this way because of me name, for they do not know the one who sent me.
John 15: 18-21