Sure:
Example one:
I have friends that works in one of the major social sites (not saying the name), and they tried ruby on rail, but failed to scale with it, both feature wise (modilarity), and sheer performance.
They tested side by side, and they had to add almost x2 the amount of servers for the same funcionality.
The mantra of Ror, is computers are cheap, developers/getting into marked is more important. When you are serving millions of users, that mantra quickly becomes expensive and hard to maintain.
They tried this in 2007, and still use ROR in limited capabilities (for some tools).
Example two:
Encoding video for potentially hundreds type of formats, for thousands of users at the same time. This is on demand video serving to customers where they have to scale in a two dimensional way (both users, and video formats). Even not trendy among many people in here, Java has one of the best and most advanced multi threading capabilities out there, especially with Java 6. So, they stuck with java for this part of functionality, and actually using Ror only for the wap front end.
Example 3:
Any custom search engine, api engine, anything that doesn't fit the CRUD mantra.
Sure you can modify Rails and get it to work for all the above examples, but it will be probably a poor fit for it. A different technology/framework, or just build your own web app without a full blown framework are better choices.
I hate it, when many people equate Web Apps with CRUD Apps, which I think it is a mistake.