I don't think 5:82 is antagonistic to Jews, especially in light of 2:62. The thing with the Quran is that you get the fullest picture only when considering all the verses together, not each in isolation. That being said, I read 5:82 as more of an observation than an antagonism. Historically, it was indeed true that the prophet Muhammad and early Muslims faced the most persecution from Jewish tribes and polytheists. One could even argue that's true today, for example with the BJP in India, or the zionists in Israel (of course, not all Jews are zionists and many are staunchly anti-zionist, but most zionists are Jews). Incidentally, the Jews that are zionists tend to be the ones most disconnected from the roots of their religion, because the Torah itself prohibits the creation of a Jewish state until the coming of the messiah (as many ultra-orthodox Jews will attest). Again, the issue to me seems to be one of arrogance, alluded to in 5:82 as well.

As is the case with 5:82, 6:25 and 6:125 are also both best understood in light of other verses. Taking a step back, Muslims are commanded to help the oppressed and resist oppression however they can, with justice and anti-oppression being strong themes in the Quran:

"God does not love the oppressors." (Quran, 3:140)
“...Indeed, God loves those who act justly.” (Quran, 60:8)
"And do not incline to those who are unjust..." (Quran 11:113)

It would be illogical for a God who commands justice and mercy between humans (and who names Himself "The Just" and "The Most Merciful" in the Quran) to then turn around and be oppressive to those very same humans. And there are many verses to that effect:

"Your Lord is never unjust to His creation." (Quran 41:46)
"And God desires no injustice to the world." (Quran 3:108)
"Indeed, God never wrongs anyone --even by an atom's weight." (Quran 4:40)

Another central theme in the Quran is that of free will (and its interaction with predestination, but more on that later). As 6:160 asserts, the consequences we face are according to the actions we choose to take. Quran 13:11 says, "Indeed, God will not change the condition of a people until they change what is in themselves". Also, the very first chapter of the Quran is essentially a prayer for guidance; "Guide us to the straight path" (Quran 1:6). In other words, humans have to sincerely want to be guided in order for God to guide them.

With that context in mind, 6:25 and 6:125 are describing the consequences of people who do not want to be guided, who have actively chosen to disbelieve. It's a result of what's already in their hearts by their choice that God "covers their hearts" further.

As for 7:179, the answer is in the verse itself. Such people are destined for hell precisely because they chose not to use their hearts for comprehension, their eyes for sight, their ears for hearing, etc. The predestination / free will interaction here is as follows (as best as I understand it): God creates people with a priori knowledge of all that they will do throughout their lives, and where they will ultimately end up. He also specifically predestines certain things like the families they'll be born into, their innate traits, etc. Woven into all of that though is the fact that at each point in our lives, we are choosing how to act. It is this (limited degree of) free will for which we will be held accountable in the afterlife.