We address an outstanding problem that represents a critical roadblock in the development of the Majorana-based topological qubit using semiconductor-superconductor hybrid structures: the quantitative characterization of disorder effects generated by the unintentional presence of charge impurities within the hybrid device. Given that disorder can have far-reaching consequences for the Majorana physics but is intrinsically difficult to probe experimentally in a hybrid structure, providing a quantitative theoretical description of disorder effects becomes essential. To accomplish this task, we develop a microscopic theory that (i) provides a quantitative characterization of the effective potential generated by a charge impurity embedded inside a semiconductor wire proximity coupled to a superconductor layer by solving selfconsistently the associated three-dimensional Schrodinger-Poisson problem, (ii) describes the low-energy physics of the hybrid structure in the presence of s-wave superconductivity, spin-orbit coupling, Zeeman splitting, and disorder arising from multiple charge impurities by using the results of (i) within a standard free-fermion approach, and (iii) links the microscopic results to experimentally observable features by generating tunneling differential-conductance maps as a function of the control parameters (e.g., Zeeman field and chemical potential). We find that charge impurities lead to serious complications regarding the realization and observation of Majorana zero modes, which have direct implications for the development of Majorana-based qubits. More importantly, our work provides a clear direction regarding what needs to be done for progress in the field, including specific materials-quality and semiconductor-purity targets that must be achieved to create a topological qubit.