Ikkitousen and Ergo Proxy aren't so much underground as they are overshadowed by stuff like Naruto and FMA. If you walk into a Suncoast or Best Buy anime section and look at the titles available you're likely to see lots of copies of several titles that don't get any advertisement outside of conventions or the internet (Darker than Black for instance).

Hulu has deals with some of the English publishers like Funimation (FMA, Ikkitousen, Kiddy Grade), Viz (Naruto, Bleach, Kekkaishi), and Gong (Ergo Proxy, Hellsing). The impression I get about the nature of the relationship though is that the distributors are the ones deciding what they will allow Hulu to stream from their libraries, not the other way around. The publishers know what has sold well and what hasn't and should have a lot more experience picking anime that American fans will want to see than the Hulu people would.