If you are experiencing the above mentioned problem after installing Service Pack 1 for Exchange Server 2013, then you should probably download and install this fix (KB2938053):
Describes an issue in which the Exchange Transport service cannot start in Exchange Server 2013. This issue occurs when third-party transport agents do not load correctly.
After you install Microsoft Exchange Server 2013 Service Pack 1 (SP1) or you upgrade an existing Microsoft Exchange Server 2013 installation to Exchange Server 2013 SP1, third-party or custom-developed transport agents cannot be installed correctly. Additionally, the Microsoft Exchange Transport service (MSExchangeTransport.exe) cannot start automatically. Specifically, you cannot enable third-party products that rely on transport agents. For example, you cannot enable anti-malware software or custom-developed transport agents. When the installation fails, you also receive an error message that resembles the following: The TransportAgentFactory type must be the Microsoft .NET class type of the transport agent factory.