Why were the colonies "unfairly represented" in Parliament?

It's not so much that the colonists were unfairly represented in Parliament; they weren't represented at all, and this was a major point of contention between the Americans and the British. A growing number of American colonists believed that it was unfair that they continued to pay taxes without being represented at Westminster (evident in the rallying cry, "No taxation without representation!").
The British, however, were largely unsympathetic. Most people in Great Britain of wealth and property—at least by American colonists' standards—weren't represented in Parliament either, and the British government pointed out this fact as evidence that the colonists were not being denied their rights as British citizens.
Additionally, they argued that the Americans already enjoyed a substantial degree of control over their own affairs and therefore didn't require the kind of formal representation in Parliament that so many of them sought. But this argument became less convincing the more the British began tinkering with the system of colonial self-government, imposing higher taxes and taking a number of steps—such as the notorious Stamp Act—that greatly antagonized the American colonists.