Self-assembly plays an important role for a variety of structural materials in biology and engineering. The underlying principles are well-known. However, the conformations and physical properties of mesoscopic structures formed are sensitive to the chemical architecture of molecular entities and the complex interplay of interactions between them. The ionomer molecules considered in our study form the polymer electrolyte membranes (PEM) that are used in fuel cells. The ionomer moieties are comprised of hydrophobic backbones, grafted with pendant side chains that are terminated with anionic headgroups. We have explored the assembly of these comb-like macromolecules using a coarse-grained molecular dynamics (MD) approach. Our study rationalizes conformational properties of backbone chains and localization of counterions as functions of side chain length, grafting density of side chains, and counterion valence. Self-assembly of hydrophobic chains yields bundle-like aggregates with a core of backbones, surrounded by a surface layer of charged anionic headgroups and a diffuse halo of counterions. The aggregate size depends on the sidechain length and grafting density and it exhibits a non-monotonic dependence on the Bjerrum length. Our study revealed different growth regimes of bundles. Results are rationalized on the basis of the interplay of electrostatic and hydrophobic interactions, as well as steric effects. Molecular-level knowledge gained through these studies is vital for rationalizing water sorption behavior, transport phenomena, as well as the chemical and mechanical stability of ionomer membranes.