The structure of low-energy collective states in proton-deficient N=28 isotones is analyzed using structure models based on the relativistic energy density functional DD-PC1. The relativistic Hartree-Bogoliubov model for triaxial nuclei is used to calculate binding energy maps in the $beta$-$gamma$ plane. The evolution of neutron and proton single-particle levels with quadrupole deformation, and the occurrence of gaps around the Fermi surface, provide a simple microscopic interpretation of the onset of deformation and shape coexistence. Starting from self-consistent constrained energy surfaces calculated with the functional DD-PC1, a collective Hamiltonian for quadrupole vibrations and rotations is employed in the analysis of excitation spectra and transition rates of $^{46}$Ar, $^{44}$S, and $^{42}$Si. The results are compared to available data, and previous studies based either on the mean-field approach or large-scale shell-model calculations. The present study is particularly focused on $^{44}$S, for which data have recently been reported that indicate pronounced shape coexistence.