One important fact about the eigenvalues of the stiffness-matrix may be the following: every system which reaches an instability-point (e.g. a buckling point) has at least one zero-eigenvalue.
Eigen values of a stiffness matrix tell you about the stability of a system and also the amount of stretching in each (eigen) direction corresponding to that eigen value.
Any square matrix of order n can be 'decomposed' into n parts using the system of spectral decomposition. This is what explains the physical significance of characteristic roots of a matrix. Now for your matrix, you can have explanations accordingly.
If your stiffness matrix of size n comes from the discretisation of a partial differential equation, then the eigenvalues of this matrix approximate first n eigenvalues of the continuous operator. These are the eigenfrequencies (free vibration modes) of the continuum system.
Very simple manner we may think if we apply a dynamic force or displacement to system of a frequency same as Eigen frequency of a system then it shows maximum response.