In the ePub exporting of InDesign CS5.5, table header rows were converted to <thead>, body to <tbody> and footers to <tfoot>. The export order is <thead> <tfoot> <tbody> -- as required by W3C (Tables in HTML documents) -- but since I found that (1) some ePub viewers were (uh...) "stupid" and rendered the elements in that order, and (2) none of the ePub viewers seem to mind my fix, I fixed this in post-processing and moved the <tfoot> after the <tbody>.
Since CS6, however, table footers are not converted into <tfoot> elements anymore! As I did not need its newer ePub export functions anyway, I stuck to CS5.5. But even though CC 2014 has improved ePub exporting, my tables are still missing their <tfoot>s!
As far as I can see, I'm doing everything right in creating the tables. Perhaps I'm missing some export setting?