The Qur'an tells Muslims to treat others differently - "Do not take unbelievers for friends and allies". Negativity towards unbelievers is expressed hundreds of times. The Qur'an is built on differentiating believer from unbeliever.
So do other religious texts or rules. Just as a random example, Exodus has "Never suffer a witch to live". My Wiccan friends would be legitimately concerned if we're to assume that Christians and Jews all take that statement literally.
It seems there are question about the interpretation of that Qur'anic line, and that it doesn't actually mean friends, but regardless, it is obvious that is not how many Muslims interpret it given they routinely have non-Muslims as both friends and allies.
You have the cause and effect backwards. I didn't have a negative opinion of Islam until I read the Qur'an. The verses I quote do not "support" my position - they created it.
What inspired you to read it in the first place though?
Define good. When 9:29 tells them fight the unbelievers until they surrender, they call doing so 'good' because their god demands it of them. I don't call it good.
That is for then to do if they care to. Again though, all of this applies equally to the scripture of pretty much any religion.
I only know what they're told to believe and do.
Well, you know what you've read and interpreted from the scriptures. You don't know what people have actually been told nor what they end up believing because (or in spite) of that teaching.
For example, I considered a Muslim co-worker a friend until he told me that he admired Hitler for what he did to the Jews. Until he said that, I had no idea he felt that way.
That isn't really about him being a Muslim though. There are all too many people who might feel the same way, either based on their religion beliefs or not.
If you're honestly not treating people differently when you learn (or think you learn) of their being Muslim, consciously or subconsciously, you're not being Islamophobic. The problem here is that you appear to be making an argument in favour of doing that, because of these negative quotes you can take from the Qur'an, there is reason to have some level of default doubt about anyone you perceive as being Muslim. That is where you can fall in to the kind of undue discrimination that would commonly be labelled Islamophobic.