Latent factor models have been widely used to analyze simultaneous recordings of spike trains from large, heterogeneous neural populations. These models assume the signal of interest in the population is a low-dimensional latent intensity that evolves over time, which is observed in high dimension via noisy point-process observations. These techniques have been well used to capture neural correlations across a population and to provide a smooth, denoised, and concise representation of high-dimensional spiking data. One limitation of many current models is that the observation model is assumed to be Poisson, which lacks the flexibility to capture under- and over-dispersion that is common in recorded neural data, thereby introducing bias into estimates of covariance. Here we develop the generalized count linear dynamical system, which relaxes the Poisson assumption by using a more general exponential family for count data. In addition to containing Poisson, Bernoulli, negative binomial, and other common count distributions as special cases, we show that this model can be tractably learned by extending recent advances in variational inference techniques. We apply our model to data from primate motor cortex and demonstrate performance improvements over state-of-the-art methods, both in capturing the variance structure of the data and in held-out prediction.