Geoffrey Parker writes a lot about Philip II, and noted that some of his biggest failures came after his greatest triumph, the conquest of Portugal. This convinced him of his infallibility; whereas he had been previously quite cautious and willing to let his agents 'on the spot' direct affairs according to their knowledge, he refused to accept argument from his subordinates, which led to defeats in France, the Netherlands, and the English channel. If Philip and Mary's union butterflies away King Sebastian of Portugal's death, then it's possible that the Habsburgs could sweep away the last vestiges of opposition.
AFAIK Philip II was a workaholic with a 'Protestant work ethic'

, but prone to micromanage too many things. I don't disagree, that after gaining Portugal, he started to believe too much in himself.
Also whereas his father Charles was basically always travelling, he didn't do that often enough. Last time Philip II was in the Habsburg Netherlands was in 1559, when he left, he made a promise to the nobility and more in general the Estates General, he would return one day, but he never did.
There were a number of things, which contributed to the Dutch revolt, not just religious*, in fact Dutch Catholics weren't pleased with the representatives from their Sovereign Lord either. There's high taxation, ignoring the traditional rights of the Estates (and provinces), local nobles saw their role in governing the region being diminished etc. And then there's the elephant in the room, that Philip II, unlike Charles V (of Ghent), basically was a foreigner and didn't command the same degree of loyalty as his father, who was a native of the Burgundian Netherlands. It didn't mean Charles V never had conflicts, but he had a much better understanding of the region, so he was better equipped to settle conflicts here.
(*= one might argue, that certainly initially, the revolt and the religious conflict were two parallel conflicts; it's only after the religious one radicalised, that lines really started to get blurred)