Not disbelievers but idolaters or polytheists. This part refers to the polytheistic arabs of Mecca with whom Muhammad was at war.
Indeed. But again, even for those, only as long as they attack or oppress the Muslims.
As a historical note: Muhammad wasn't treated as just yet another leader of yet another nutter sect. As soon as he started preaching against the idolatry that was the official religion, the reaction was (unsurprisingly) _very_ negative.
As the number of his followers grew, and basically started to be a credible threat to the status quo, that turned to persecution. And I mean "persecution" as in: people were killed, and some even tortured to death. (Although Muhammad himself seems to have been spared any physical violence to avoid a feud with his clan.) Soon muslims started emigrating just to keep their lives, culminating with the whole sect moving to Medina.
At that point, Mecca took the time to make itself even more of a dick and confiscated the wealth of all muslims. Which, needless to say, didn't make those love the polytheists of Mecca any better.
In response to that injustice, the emigrant muslims started attacking the caravans to/from Mecca. (Which also puts the "OMG, Muhammad was a bandit" propaganda point into context. Those guys didn't raid everyone's caravans or anything.)
Mecca responded by sending soldiers, which culminated in the battle of Badr, a major victory for Muhammad's forces, although estimated to have been outnumbered 3 to 1.
Mecca at that point seems to have taken that as a major loss of face -- and you have to understand that in that culture the personal and clan honour and prestige weren't just worth status, but alliances, trade treaties and hegemonies depended on it -- and started an all-out war against Medina. At the peak of the conflict an army of 10,000 (which was immense for the area: by comparison at Badr they had sent about a tenth of that, and the Muslims had been only 300) besieged Medina but failed.
The fight ended in a truce, which Mecca soon broke by funding and arming another clan to attack Medina. Muhammad wasn't amused with the situation of having a truce but being attacked anyway, and asked that Mecca chooses one of three outcomes:
1. they pay reparations to the families of those killed in those attacks, or
2. they disavow their new alliance with the clan attacking Muhammad, or
3. they declare the truce null and void. (Effectively putting them back into the war where they had declared war on Muhammad.)
Mecca chose #3. At that point Muhammad was in a position to raise his own 10,000 man army and basically blitzed into Mecca. (And as a proof of that, you know, lack of mercy of Islam and all, he actually pardoned all but 10 who had personally insulted him. About half of those would be pardoned anyway later.)
That's the kind of conflict where Muhammad was urging his followers to fight the polytheists. It wasn't just picking on some innocent neighbours, but on some people who had declared war on him, were killing his followers wherever they could find any, and destroying their crops.
I hardly think that self-defense is some kind of evil act, either back then or nowadays.