Optical communications provides a means of high data rate communication over the clear atmosphere provided the communication system is designed properly. This paper examines the performance of TCP and similar protocols when operated over atmospheric optical channels. We first develop a simple stochastic channel model, and use this to derive approximate transport layer protocol throughput. We found that the throughput over short atmospheric paths is nearly optimal and the throughput over medium range atmospheric paths can be made fairly efficient with the use of diversity and/or link margin. However, its throughput at high data rates (>1 Gb/s) over long paths such as from one location on earth to a geosynchronous satellite is poor even with 10 dB of link margin and 16 diversity transmitters/receivers. This points to the necessity of a new transport layer protocol without a window closing feature.