It's not brain washing because you're merely reading again to strengthen your understanding. You wouldn't read a Shakespeare play and understand it 100% in one attempt right? It's the same concept. Throughout my college years in English courses, we had to break down Shakespearian (sp?) literature to thoroughly understand them and their meanings.
Nonetheless, moving on to the article you posted. It actually made me giggle a bit. The attempt at understanding the Noble Qur'an appears to have been done in a much more open-minded manner than usual, albeit still off. Now there were a LOT of verses posted and whether I am at work or not, I couldn't possibly take the time out to translate each and every one in its proper context (referred to in Arabic as a "tafsir" -- would be best to search for a tafsir of a specific verse in Google when searching for a clear and unbiased understanding). I will, however, attempt to just apply my knowledge on the matter as a whole.
Yes, Muslims are in fact instructed to love Christians like their own siblings. Same with Judaism, but a much larger emphasis placed on Christians. The author of the article states his confusion on why the Qur'an appears to retract some of its sincere comments toward Christians.
The problem with reading translations of Arabic is that the language is very different from English in many, many ways. So translating appropriately is a very difficult task to accomplish. Essentially there are many more ways to describe something in the Arabic language than in English, hence all the different interpretations and misinterpretations. One of the duties of a Muslim in his/her life is to read the entire Noble Qur'an from start to finish in Arabic, not any other language, for this very reason.
Now as far the verses and their meanings. Lets travel back in time 1.2 millenia ago. The prophet Jesus, peace be unto him, performed many miracles and for so-and-so reasons became a threat to the Holy Roman empire. After being sentenced to death, Christians and Jews believe he died on the cross but Muslims believe God brought his living body to safety in Heaven and has always remained alive (hence being able to return as the Messiah during the End Times), and the person placed on the cross was an exact look-alike of the prophet. This is where difference #1 between Christians and Muslims stemmed from.
As we all know, A.D. is either Anno Domini or After Death in reference to the prophet Jesus, obviously making '0' the year he left this world one way or another. Exactly 312 years later, the Council of Nicaea declared he was the Son of God. Hence, you have the foundations of Catholicism and separation from mainstream Christianity. Who would have written about the true story of Jesus? As you said, the victors write history. Many people began worshipping him as the son of God or being God Himself, even praying toward idols of him.
This poses three huge problems in Islam. Islam does not recognize idolatry or polytheism as any form of truth and that God is only One with no children or equals. Some may disagree saying Catholicism isn't practicing idolatry, but when praying toward an idol depicting the appearance of a deity to either send/receive blessings, it becomes idol worship.
The prophet Muhaofftopicd, peace be unto him, was an illiterate yet highly intelligent and respected man of little stature in a small, remote village. One day, he was approached by the angel Gabriel during his routine trips to a nearby mountain to meditate. It was there in disbelief that he was forced to accept the words of God and slowly over time, was revealed the entire truth of the original and untainted Christianity now renamed as Islam. It became his duty to become a leader and spread that message to his community which was met with much hatred. Eventually, he and his followers fled to a nearby kingdom under the kingship of a righteous Christian king who placed them on trial along with those chasing Muhaofftopicd's followers. It was there they recited to the noble Christian king verses from the Qur'an about the virgin Mary and her son, the prophet Jesus. Astonished and baffled, he said the exact words while pointing at 2 rays of light peering into the court room, "Islam and Christianity are like these two rays of light. Parallel yet apart. I would not give these men to you for a mountain of gold" aimed toward the captors. It was here where the first interaction between Islam and Christianity was established and remained in positive relation until the Crusades a few centuries later.
With that said, now being able to properly answer your question, Islam recognizes that the Bible was eventually misconstrued and gone away from its original intent/meaning, creating different sects of Christians. This is why you have the noble Qur'an speaking highly of Christians in one verse and may appear to be speaking ill of them in another. The references are actually between true Christians who share near identical beliefs with Muslims and then the Christians who began following a new religion and adopted the prophet Jesus as God or the son of God.
Overall, just know that regardless of faith, Islam teaches us to become leaders and treat all people, even our enemies with the utmost respect. A tiny example from the Noble Qur'an on how it is against acting out of compulsion is during one of the Muslim's first few battles to defend themselves, a Muslim warrior knocked his enemy down to the ground and was about to slay him with his sword. His enemy, clearly defeated, expressed his utter disgust by spitting on the Muslim warrior's face. The warrior stopped for a moment and pulled his sword back and stepped away. The defeated man asked why he didn't slay him and the Muslim replied that if he killed him at that point, he would have committed a sin because his action would then have been out of anger and not duty.
By the way, this is the same for Jews. Islam does not recognize Zionist-Jews because they re-wrote the Torah in favor of their own personal gain, yet it does recognize original Judaism.
