The self-assembly of surfactants into lyotropic liquid crystalline phases is interesting from a fundamental and practical perspective. The propensity for self-assembly is particularly interesting in Gemini surfactants which have a very low critical micelle concentration. In this work, we study the effect of headgroup identity on the driving force for the self-assembly of Gemini surfactants, using computer simulations of the potential of mean force (PMF). We find that surfactants with sulfonate headgroups have a greater tendency to assemble than those with carboxylate headgroups. The minimum in the PMF is about a factor of 2 deeper and occurs at shorter distances. Interestingly, the driving force is entropic with the carobxylate and energetic with the sulfonate headgroups. Analysis of different contributions suggests that these differences arise from surfactant headgroup electrostatics and size. The results provide an explanation for why the morphology diagram of the sulfonate surfactants is insensitive to temperature.