I think show length is a major factor in this too - I'm glad you brought that up. It's part of why I was sad that the theater at MK got axed (or is that just temporarily on hold or...I can't keep track of it all anymore, lol)...
At any rate...When you look at Indiana Jones and say it holds 2,000 people...well between showing up a little early and the time to exit the theater that keeps those 2,000 people busy & entertained for an entire hour basically. When you look at a ride with a similar capacity (say Rock'n'Roller Coaster) between pre-show and ride those people are only occupied for 8-10 minutes. Now of course RnR has a long line too which keeps those people busy for an hour or more probably.
I guess it's hard to compare short rides with long lines to long shows with no lines...but I don't mind Disney having some high quality shows that take thousands of people out of the mix and when I watch allow me to get off my feet for 45 minutes or so.