When in the Quran, Allah commands certain acts, like fighting against certain groups of disbelievers of Islam, these verses were specifically for the disbelievers at the time of the Prophet, who were killing and oppressing Muslims and turning them out of their own homes, simply because they refused to worship other God's besides Allah, and give up their faith. It's not to mean all disbelievers of Islam in general and certainly not non Muslims who do us no harm.Likewise some verses in the Quran were abrogated with the coming of others.
And for anyone to know this it's essential to study the Quran with it's authentic explanation, and not simply try to interpret it on your own.