I will try and explore what I believe God meant by Quran 3:28 In order to find out what God meant by the verse it is important to quote the verse in question:
Translation of Quran 3:28 by Muhammad Al-Hilali & Muhsin Khan:
Let not the believers take the disbelievers as Auliya (supporters, helpers, etc.) instead of the believers, and whoever does that will never be helped by Allah in any way, except if you indeed fear a danger from them. And Allah warns you against Himself (His Punishment), and to Allah is the final return.
The reason why I choose the above translation is because this one is the clearest as it has used the actual Arabic term and put the translator's interpretation of the meaning of the word in brackets.
We have already established in the previous post of what auliya means.
Tafseer Summary
The common theme throughout the tafseer's quoted below was the context of when this verse was revealed, according to the tafseer by Wahidi some Jews kept close to the helpers (which refers to those Muslims in Medina helping the Muslims who migrated from Mecca due to persecution to integrate into society in Medina) in order to make these Muslims lose their faith. This is a good reason for God to reveal this verse to warn the believers not make friends, allies, patrons etc with (such) unbelievers as God is good and that is God's "job" to advice the believers in what is right (after all why would God allow His sincere servants to go astray out of ignorance of what is going on?), whether the believers take notice and act on this guidance, that is up to them as there is no compulsion in religion.
Another thing which the tafseers point out was that some of the hypocrites (who were Muslim outwardly but did not believe inwardly) such as Abdullah Ibn Ubay and his companions mentioned by the last 2 tafseers, tried to supply information to those who were against the Prophet (pbuh) such as (some) Jews and (some of) the pagans in order to help them against the Prophet (pbuh) and to become mighty and honourable (possibly referring to being might in the eyes of the unbelievers?), rather than being pious and sincere in the eyes of the Muslims.
So to sum up: from what I understand this verse does not prohibit Muslims making friends with non-Muslims, but rather it warns Muslims from making friends, patrons etc with unbelievers (non-Muslims and hypocrites) that try to deliberately make you lose faith in Islam, and those hypocrites who are helping non-Muslims in their cause to make you lose faith in Islam in order to gain honour in the eyes of non-Muslims rather than trying to increase the faith of the Muslims.
Tafseer's on Quran 3:28
Here is a tafseer by Jalalayn:
Let not the believers take the disbelievers as patrons, rather than, that is, instead of, the believers — for whoever does that, that is, [whoever] takes them as patrons, does not belong to, the religion of, God in anyway — unless you protect yourselves against them, as a safeguard (tuqātan, ‘as a safeguard’, is the verbal noun from taqiyyatan), that is to say, [unless] you fear something, in which case you may show patronage to them through words, but not in your hearts: this was before the hegemony of Islam and [the dispensation] applies to any individual residing in a land with no say in it. God warns you, He instills fear in you, of His Self, [warning] that He may be wrathful with you if you take them as patrons; and to God is the journey’s end, the return, and He will requite you.
The following is a tafseer named as Tanwir al miqbas min tafsir ibn Abbas:
(Let not the believers take) the believers ought not to take [the hypocrites:] 'Abdullah Ibn Ubayy and his companions [and] (disbelievers) the Jews (for their friends) so as to become mighty and honourable (in preference to believers) who are sincere. (Whoso doeth that) seeking might and honour [by taking the hypocrites and disbelievers as friends] (hath no connection with Allah) has no honour, mercy or protection from Allah (unless (it be) that ye but guard yourselves against them) save yourselves from them, (taking (as it were) security) saving yourselves from them by speaking in a friendly way towards them with, while your hearts dislikes this. (Allah bideth you beware (only) of Himself) regarding the shunning of unlawful killing, unlawful sex, unlawful property, consuming intoxicants, false testimony and associating partners with Allah. (Unto Allah is the journeying) the return after death.
The following is a tafseer named as Asbab al Nuzul by Al Wahidi:
(Let not the believers take disbelievers for their friends in preference to believers…) [3:28]. Said Ibn 'Abbas: “A group of Jews including al-Hajjaj ibn 'Amr, Kahmas ibn Abi al-Huqayq and Qays ibn Zayd used to keep close company with a group of Helpers to try to make them renounce their religion. And so a group of people comprising Rifa'ah ibn al-Mundhir, 'Abd Allah ibn Jubayr and Sa'id ibn Khaythamah said to this group of Helpers: 'Stay away from these Jews and beware of keeping their company lest they drive you away from your religion'. The group of Helpers refused to stop seeing them or keep their company, and so Allah, exalted is He, revealed this verse”. And al-Kalbi said: “This verse was revealed about the hypocrites: 'Abd Allah ibn Ubayy and his companions. They allied themselves with the Jews and the idolaters, supplying them with information, hoping that they would have the upper hand over the Messenger of Allah, Allah bless him and give him peace. And so Allah, exalted is He, revealed this verse, warning the believers against acting like them”. Juwaybir reported from al-Dahhak that Ibn 'Abbas said: “This verse was revealed about 'Ubadah ibn al-Samit who was among those who took part in Badr and a trusted man. He had allies from among the Jews. And when the Prophet, Allah bless him and give him peace, marched to the Battle of the Confederates, 'Ubadah said: 'O Prophet of Allah! I have with me five hundred men from the Jews, and I am of the opinion to take them with me to impress the enemy. Because of this, Allah, exalted is He, revealed (Let not the believers take disbelievers for their friends in preference to believers)' ”.
If I have said anything you disagree with, or anything is incorrect please let me know, so I may look further and If I find that in my research that I was incorrect then I will correct anything that I had written, God willing.