Assuming Spain won't annex England (and I believe they weren't planning to), England wouldn't be finished. It would still exist, but with a catholic king. It would rule a very unhappy population and would be busy keeping them under control and possibly get involved in religious wars on the continent. Maybe a English civil war starts. This all might keep England too busy to colonise for decades, maybe even more than a century. At that point the Portuguese, French, Dutch (having a large part of the Spanish army fighting in England instead of the Netherlands is very good for the Dutch), Danish, Swedish and maybe even the Scotish might all fill the gap the English left open.
Philip wanted to put his daughter Isabella on the throne. You're right that she would be very unpopular, but I don't think that England would burst into spontaneous constant rebellion like the Netherlands. Rather there would be a "political war" for control of the Church of England and the tuition of any children of Isabella's. Otherwise, the Protestant nobles would just retreat from court and the people would just become more desensitised to politics, as a portion of the population did with religion. At any point of weak rule (i.e. a malleable monarch or a child king) Protestant nobles would step in, outnumbering the Catholics as they did, to try to engineer a Protestant education to restore the new faith, and to reinstate reformist priests in the bishoprics. Spanish troops might be called in for the Queen's protection but England wouldn't absorb loads of tercios and make the job easier for the Dutch.
Either way, remember that colonisation in this era was not state organised. Colonies were founded by enterprising gentlemen raising funds, obtaining a charter, and then organising the work themselves. Of course, the major problem is that a Hapsburg monarch won't sanction any English colonisation as the Hapsburgs believed whole-heartedly in the Treaty of Tordesillas which promised 99% of the Americas to Spain. If they could get around that, though, a monarch disinterested won't stop colonisation. Remember that the eastern seaboard wasn't properly colonised until the period of 1650 to 1700, which gives plenty of chance for the English to recover even from a Hapsburg puppet monarch.
I think you're exaggerating thinking the Danes and Swedes will become major players given England's absence, by the way. They were never that interested in colonies, they didn't have the strength to really become major overseas players and they didn't tend to focus on North America anyway, instead choosing small spice islands to hold as isolated outposts. Exception goes to New Sweden, but this proves my second point - against the Dutch, French, etc they were never strong enough overseas to protect their investments. English non-colonialism will only strengthen France and the Dutch. Scotland definitely won't colonise. It just didn't have the ability. The Scottish economy was a joke in this period - a lot of sources refer to it, even in 1707 when it joined the Union with England - as being the economically poorest country in the whole of Europe. It had no real successful industries, no decent products to trade, a small population with little interest in forming colonies even in the few who had the money to, and furthermore, again no military ability to defend the said colonies. Scotland could have tried colonising but IRL it didn't even try until 1706 and there's no reason to assume that if England were reduced to a menial existence that Scotland would do any differently. In fact if we are to take your initial suggestion that a defeated England would resign itself to an existence picking on the Scots and Irish, then the devastated Scottish economy would make 100% certain that Scotland could never attempt any colonialism.