This rang alarm bells with me, because my work is highly interdisciplinary. It combines agricultural ecology, protein chemistry, and archaeological artefact studies. So if this is true, then I should be very worried. I have now published 4 peer reviewed papers as first author (where I dealt with reviewers comments directly, so I know what was in them), and it is true that the only one that was rejected (from 3 journals, no less) was the one that combined archaeology and science most intimately. Two of these journals were mid/high-impact general science journals, and one was a high-profile archaeology journal (high for archaeology that is...), so it is possible that we were being too ambitious with it.
So I asked my peer group for their thoughts on this issue. They made the following points:
1. It's different in America
In America, archaeology is seen as part of anthropology (that is, definitely a social science), rather than as somewhere between history and geography (so partly a humanity and partly a science). The basic expectations of its inter- or trans-disciplinary nature are therefore different.
2. Combining science with archaeology is different to combining sociology with archaeology
Archaeologists have been writing about how to combine scientific thinking with archaeology for a while now. The general consensus seems to be that they are different but can be combined. An introductory textbook to archaeological theory includes a chapter on "archaeology as a science". In Great Britain, there is a particularly strong association between archaeology and the sciences, and there are a number of international journals dedicated to science in archaeology. My work therefore nicely into the mental bin marked Scientific Archaeology. There is no such bin for Sociological Archaeology, despite the fact that anthropology is, for many, part of sociology, and although archaeology has nicked plenty of theories from sociologists, most repetitiously Marx.
3. Inter/trans-disciplinarity is more difficult than sticking to one discipline
Because you've got three times as much reading to do, and will inevitably have a lesser familiarity with every aspect of all combined disciplines than a mono-disciplinary scholar would have of their single discipline. So it shouldn't be surprising that genuine problems in work of this nature can be picked up at peer review in a discipline-focused journal.
The corollary on the journal side is that inter-disciplinary work is more difficult to review adequately, as journal editors need to go beyond their typical reviewer pool and bring in people from outside the discipline to assess the work. (I don't mean that all editors have limited stables of preferred reviewers, rather that they know how to assess the suitability of people to review in their own discipline, and may not in others).
4. Two fingers to the fuddy-duddies
Yes, some academics are lazy and parochial. Don't let them stop you if the work is good.
All of which I will be taking to heart as I get an isotopes/textiles paper ready for publication... Kudos to Lisa, Steve, Freder and Kathryn for their generously shared wisdom and skepticism.