"Fight those who do not have faith in Allah nor [believe] in the Last Day, nor forbid what Allah and His Apostle have forbidden, nor practise the true religion, from among those who were given the Book, until they pay the tribute out of hand, degraded." - Qur'an 9:29
At first glance, if you are to selectively read certain passages in the holy Quran, or in the Bible or any other scripture, you might see it to be violent, offensive, or maybe even unethical.
Of course, this is an unfair assessment, especially when there is a strong emphasis on the necessity of understanding the sequence of historical events that, for example, surrounded that verse, or to look at the other verses that speak exactly the opposite of what you just read.
There are important tools that must be used when reciting the Quran, and one of them is called Tafseer. This is the exegesis and commentary that explains the background story to the verse, or the event, and gives an overall explanation to what the text refers to.
I would advice you to see what our tafseer books say about this particular verse, and also what mainstream Islamic scholars say as well.
If you have time, please watch my lecture I delivered a few years ago on this topic: