What is the root of unhappiness in this book?

The root of unhappiness, according to Marx and Engels in The Communist Manifesto, is the alienation of the working class, or proletariat, from the fruits of their labors. Marx and Engels describe all of history as a class struggle, one that is reaching its conclusion with the advent of industrialization. The development of industry has crystallized social structures into two classes. The proletariat, which constitutes the vast majority of humanity (or at least people who worked in industrialized societies) is one. Opposing them is the bourgeoisie. They are the wealthy people who controlled the means of production, and constantly tried to squeeze as much profit as they could out of their businesses and the people that labor for them. In the preface to the Manifesto, Marx and Engels describe the bourgeosie's relationship with the proletariat as "naked, shameless, direct, brutal exploitation." This is because, more than previous dominant classes, the bourgeoisie was driven purely by the profit motive. This outweighed any moral or ethical concerns business owners may have had, and encouraged them to view their workers simply as economic units.
The authors did not suggest that there had not been human misery, nor exploitation, nor unhappiness before the rise of industrial capitalism. They claimed, however, that capitalism had worsened, or intensified inequalities to the point that they were unbearable for people. Because the profit motive was the cause of all of this, it would only get worse, as the bourgeoisie constantly invented new ways to make workplaces more efficient and "rational" in their exploitation of human labor and their generation of profits. Fundamentally, what was happening was that the working class was generating more and more wealth, and seeing proportionally less and less of it. This was the source of unhappiness for the working class, and Marx and Engels predicted that eventually, or even in their own time, the proletariat would attain class consciousness, or an understanding of the roots of their predicament. When this happened, they would inevitably overthrow the bourgeoisie. The Communist Manifesto is intended to help workers understand the source of their oppression, and to inspire them to do something about it.