The first three can reasonably be thought of as defining linear transformations. For linear systems of equations A x = b, x is an unknown vector in the input space that is mapped by A to b.
Both covariance matrices and Hessians are more naturally thought of as tensors, not matrices (and therefore not linear transformations). That is, they take in two vectors as input and produce a single real number as output.
As for graph adjacency matrix, this can actually be thought of as a linear transformation on the vector space where the basis vectors correspond to nodes in the graph. Linear combinations of these basis vectors correspond to probability distributions over the graph (if properly normalized).
2D images... Yes, these cannot really be interpreted as linear transformations. But I'd say these aren't really matrices in the mathematical sense.