Joe Carter points to an interview with sociologist Rodney Stark (who is not a historian, despite often being called a historian of religion) that complains about the use of the word "mainline" in the expression "mainline Protestant denominations". This term usually refers to the more liberalizing denominations within each major Protestant grouping. So for Presbyterians, it means the PC-USA. For Methodists, it's the United Methodists. For Baptists, it's the American Baptists. For Lutherans, it's the similarly-ironically-named Evangelical Lutherans (who are much less evangelical than the Missouri Synod). Episcopals are usually seen as part of this group, and the United Church of Christ is also commonly included.
Stark's point, which Joe agrees with, is that these groups aren't really mainstream anymore. They're dying off. As they shed central and historic beliefs of Christianity, they become less mainstream within Christianity. I fully agree with that observation, but I think it's a mistake to complain about the use of the term "mainline".
What's going on here, as I see it, is that the term "mainline denominations" no longer functions as a description. It functions as a name. So in terms of the semantics of the expression, it doesn't really matter that it's ceased to be informative. It's like complaining that you park in driveways and drive on parkways. It's an interesting irony in the etymology of such terms, but it's not a problem with the language. Names often originate in circumstances that make their etymology seem ironically opposite to their current reference. The problem is not that anyone uses the term to refer to the groups it refers to. The problem is if they, in so doing, think they're using the name as a description rather than as a name.
It's wrong to think the mainline denominations are all that mainstream. I suppose it's true that they're closer in their ethical and theological outlook to secular America than the more evangelical congregations and denominations are, but there's enough counter-cultural Christianity present that large swathes of them are not mainstream in that sense. But they're not as mainstream Christianity as the more evangelical congregations and denominations are (and when I say "more evangelical" I mean it; it comes in degrees). Stark is right about that. But that doesn't make it illegitimate to continue to use the name for the group it's come to refer to any more than it's wrong to continue to use the name "Rhode Island" to refer to the entire state, even though it originally was only ever meant to refer to the island that constitutes Newport, Portsmouth, and Middletown. The name has come to refer to the entire state, and its inaccuracy as a description doesn't change the fact that it does refer to the whole state.