Yeah, Marx wants the entire bourgeoisie overthrown—but for him, there's actually more than one kind of bourgeoisie, or at least there are different shades of bourgeoisie.
The petit—French for small—bourgeoisie is made up of small business owners. These people hire other workers, and hence benefit directly from the appropriation (or, in Marx's view, stealing) of the proletariat's wage-labor, but they generally do not own large-scale means of production. So, a grocery-store owner would be petit bourgeoisie, because he benefits from the value added by the labor of his workers but doesn't own an oilrig or a bunch of land.
An interesting example might be a small-fry, self-employed freelance journalist in what today is called the knowledge economy (as opposed to Marx's industrial age). The journalist owns a computer and office equipment, which are arguably means of production, even if small-scale. He or she might also "hire" unpaid interns—a kind of employment, sort of—whose labor he benefits from for free.
On the other hand, as a little-known journo, he or she is probably paid an average of only about $200 per article before self-withholding for taxes, which is certainly not what you expect a member of the bourgeoisie to be living off of or re-investing.
The question of classifying the petit-bourgeois points to the boundary problem Marx's class analysis raises: where do you draw line as to who belongs to which class? Marx seems obsessed with looking at the world in terms of economics—wage-labor versus capital, for instance. But what about a male journalist, for example, being able to win more article assignments from magazines than a female journalist, simply because of the over-representation of males in the media? The Manifesto says next to nothing about this factor in classification; see our "Women and Femininity" theme for more on that.
Don't Be So Petty
Another point Marx would raise about the petit bourgeoisie is that they're at risk of becoming proletarians due to the increasing power of the bourgeoisie, who centralize wealth and influence the government to pass laws in their favor, pushing everyone else downward economically.
In Marx's words, "The lower strata of the middle class—the small tradespeople, shopkeepers, and retired tradesmen generally, the handicraftsmen and peasants—all these sink gradually into the proletariat, partly because their diminutive capital does not suffice for the scale on which Modern Industry is carried on, and is swamped in the competition with the large capitalists, partly because their specialised skill is rendered worthless by new methods of production. Thus the proletariat is recruited from all classes of the population" (Section1.35).
Capitalist economists would argue otherwise: that if the rich get richer, the poor get richer, too, as in the saying that a rising tide lifts all boats.
Today, both the bourgeoisie and petit bourgeoisie can be contrasted against the labor aristocracy. The labor aristocracy is made up of workers who have managed to negotiate pay for themselves higher than the value they add by their labor. Although labor aristocrats don't benefit from the wage laborer directly—since labor aristocrats don't hire the wage laborer and then keep a portion of the value the laborer adds to the product—they do benefit indirectly by having the purchasing power to buy the goods the laborer makes but cannot afford.
They also benefit indirectly in the sense that the higher wages they're paid for their labor are only made possible, Marx would say, by the wages stolen from the value added by the wage-laborers on the bottom.
Marx, in fact, might say that many workers in the United States are labor aristocrats compared to workers in the third world such as child miners in Africa, since the former are able to maintain a lifestyle the latter can't and can do so only because of the great inequality between workers in the U.S. and the third-world workers they indirectly exploit.
So, would Marx endorse the third world simply overthrowing the entire United States? Is his class analysis and call for revolution a fair reckoning of long-standing injustice, or is it so crude and simplistic that it would lead to more problems than it would solve?