According to Marx and Engels, the bourgeoisie spreads civilization by being so efficient at creating material goods. By doing this so efficiently, bourgeois countries force other countries to become civilized or die.
Basically, Marx and Engels are talking about globalization here. They say that the bourgeoisie have gotten to be so good at making and transporting things that there can be nowhere that is out of their reach. Because the bourgeoisie can make so many things and transport them so far, they are able to put pressure on all the countries of the world to become part of the civilized, capitalist system. By doing these things, the authors say, the bourgeoisie
... compels all nations, on pain of extinction, ... to introduce what it calls civilization into their midst...
So, when Marx and Engels say this, they are not lauding the bourgeoisie for improving other countries. Instead, they are saying that the bourgeoisie forces all other people to become part of a capitalist civilization.