What's up with travel sites?

So, I went to Expedia.com to compare air fares to the next NCTE conference. Ok, it was a class assignment, but the point is I found myself looking at air fares. The LOWEST fare on Expedia was $697. Just for kicks and giggles, I went to the website for Southwest Airlines. The same flight, mind you. A list of about nine flights came up and the HIGHEST fare was $392. Same departure date, same seating. What's the deal? The convenience of checking six airlines at once (Southwest was not even on the list BTW) costs an extra $300? Where's the convenience if they're not going to show me the cheapest fares? I don't get it.