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Trigger warning: more mechanical discussion of nonconsensual sex.
On a per-act basis, rapes are about twice as likely to result in pregnancy than consensual sex. I suspect that you're right that various fertility-boosting measures don't happen during rape and this effect is due primarily to selection effects (who rapes, who is raped, and when the rape happens), but the net result is still that rapes are a decent reproductive strategy (if the rapist can get away with it).
This seems really unlikely in the context of marriages before the Enlightenment, or in the context of wars and raids (where women were a resource like any other).
Yes, in America. We also frequently do our best, when having consensual sex, to minimize our odds of having kids. (I was unable to find rates of birth control use during rapes, unfortunately.) In the ancestral environment, this would probably not be a factor.
I'm pretty sure the 3% number comes mostly from women trying to get pregnant, and it's estimated that the per-act incidence of rape pregnancy would be about 8% instead of about 6% if none of the victims were using birth control.
Tentatively updated. Will investigate further later. 3.1 number comes from an odd data-set.
http://www.niehs.nih.gov/research/atniehs/labs/epi/studies/eps/question/index.cfm
It looks to me like your link is a 1995 study, and my link described a 2000 or 2001 study, which I'm having trouble finding. I think it might be this one but I'm not seeing the 3.1% value anywhere. The study I linked has slightly lowered my credence in the 3.1% number, but I can't tell if the numbers it's reporting are per-act numbers or not. (I'm not an expert in this field and have been trusting summaries from science journalists; I'm not sure if I'm interpreting the actual papers correctly or not.) It looks like this study might have said "at their least fertile, there's less than a 5% per-act chance of copulation, which is lower than we thought it was" and that got interpreted as "in general, there's less than a 5% per-act chance of copulation."
I hope Gottschall and company know what they're doing, and expect the 3.1% number comes from another study. It might be profitable to email one of the professors in question and ask for where that number came from, because it's being slippery.
Sorry, for deleting my post. I linked to the wrong study (as you pointed out) and wanted no replies until I revised my post.
Also, this is the 2001 study:
http://www.ncbi.nlm.nih.gov/pubmed/11376648
Edit: I would like to criticize Todd Akin for making my truth-seeking less convenient by really messing up the signal-to-noise ratio regarding this matter.
They touch on the statistics further down -- it's believed to be due to the fact that, in the case of consensual sex, the woman is more likely to have control over when in their fertility cycle the act occurs.
Different cultures have had very different approaches to marriage throughout history; they still often do. Anyway, I'm talking about the claim that rape is an evolutionary adaptation from the ancestral environment, couched as a reproductive strategy -- Neolithic Eurasia is a bit too recent to be germane to my argument.