Some problems are linear, but some problems are non-linear. I presume that you started your education discussing and solving linear problems which is a natural starting point. For non-linear problems solutions often involve an initial processing step. The aim of that initial step is to transform the problem such that it has, again, linear flavor.
A textbook example is the logistic regression, a tried-and-true recipe for getting the best linear boundary between two classes. In a standard neural network model, you will find logistic regression (or multinomial regression for multi-class output) applied on transformed data. Few preceding layers are “devoted” to transform a non-separable input-space into something which linear methods could handle, allowing the logistic regression to solve the problem with relative ease.
The same rationale holds for spectral clustering. Rather than working with the original inputs, work first with a transformed data which would make it easier to solve, and then link back to your original inputs.
Spectral clustering is an important and up-and-coming variant of some fairly standard clustering algorithms. It is a powerful tool to have in your modern statistics tool cabinet. Spectral clustering includes a processing step to help solve non-linear problems, such that they could be solved with those linear algorithms we are so fond of. For example, the undeniably popular K-means.