Dielectric waveguides are intensively investigated as accelerating structures excited by an electron beam. Rectangular dielectric structures are used both to test the principles of new acceleration schemes and to study the electrical properties of filling materials. A number of dielectric materials used to fill waveguides have anisotropic properties (sapphire, ceramic films). Anisotropy can have a significant effect on wake fields generated by an electron beam in the structure. An analytical calculation of the Vavilov-Cherenkov radiation generated by a relativistic electron bunch in the rectangular waveguide with a transversely inhomogeneous transversely isotropic dielectric filling is carried out. A method for constructing an orthogonal basis of a transverse operator with its subsequent use to find the wake field is presented. A dispersion equation for the structure and expressions for the wake field created by a point electron bunch in the transversely isotropic rectangular dielectric structure are obtained. On the basis of the above formalism, calculations were made of the parameters of an accelerator structure based on sapphire, which permits the generation of fields above 100 MV / m.