Coating materials based on siloxane-containing polymer matrices that had been modified with fluoropolymer or acrylic resins and applied as organic components of hybrid systems were examined. The optimal recipes of the dispersion systems, applied as polymer matrix precursors, were determined on the basis of factorial experiments, designed as 22 with additional ‘star’ experimental points to obtain greater accuracy in the resulting regression equations. The siloxane cage formation was based on the following crosslinking reactions of functional polysiloxanes: (1) hydrosilylation of vinyl groups; (2) condensation of silanol groups. Moreover, the molecular modeling, using P3 semi-empirical methods, was applied to build the model structure of a siloxane-containing polymer matrix. The surface properties of these coatings were studied using wettability assessments (dynamic contact angle and surface-free energy evaluation), atomic force microscopy (AFM), and X-ray electron microscopy (ESCA-XPS). The morphology, roughness, and structural regularity are discussed to illustrate the effects of the organic component on the surface properties. The most significant changes were observed in the surface morphology of the coatings. The application properties of such coating materials for the protection of buildings were tested, based on studies of their water vapor permeability, water absorption, and weathering resistance (freezing/thawing, salt-saturated aqueous sodium sulfate solution). The effect of the chemical structure of the siloxane-containing polymer matrix on the properties of the resulting coatings was focused on the protection of porous building materials. A very good correlation of the application properties of these coating materials and their surface properties, such as high dynamic contact angle (DCA), low surface-free energy (SFE) and surface morphology, was observed and is discussed.