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In the future the amount of air traffic as well as the total data traffic volume of aeronautical communication will significantly increase. A single terrestrial technology alone will likely not be able to manage this challenge but satellite communication systems will serve as complement to direct air to ground data links. The future air traffic management (ATM) will thus consist of highly heterogeneous networks consisting of diverse technologies. It is highly important to design the network protocol stack in a way that allows interoperability of all involved networks while being transparent to the end users and providing the required levels of QoS performance, especially in the presence of transport layer protocols like TCP. This paper presents three different protocol stack alternatives dealing with the mentioned issues, investigates their advantages and disadvantages and proposes a protocol stack fitting the needs of ATM communications.