Question: What is preventing the "Exit Node" from tampering with the message going to the server, or the message coming back to the user. As far as I understand, the "Exit Node" can read the unencrypted message, and there is nothing stopping it from tampering with the message, adding some sort of Trojan?

Answer: 
The best option to avoid exits tampering or inspecting your traffic is to only use encrypted protocols over Tor exit nodes. That means HTTPS, primarily, but if you're using another protocol (such as IMAP, for checking mail, or IRC) ensure it is the "over TLS" version.
The answer is - **It can't be trusted** Tor is a network with *just* an alternative routing scheme, so you're up to **yourself** to guard your SSL, TLS and so forth... Even more: a malicious exit nodes are catched from time to time, so - unless you're maintaining a full-scale security on your side - Tor is totally not a remedy for this