While it
may have lacked some of the facts in the past (though that is disputable), we have known for some time now that the drug market is demand driven, and this demand is extremely inelastic. Basic microeconomics says that inelastic demand can be consistently profitable. No matter what we do[1],
somebody will step up to take that profit.
So we, as a country, had (and still have) a choice: who do we want managing this profitable market? Traditionally, we have chosen to fund violent gangs and cartels. We took what could have been a regulated - and taxed - market, and handed those profits to some of the worst people on the planet. So yes, there is funding going on of some bad people. That is by design - the prohibitionists even put "raising drug prices" as the purpose behind many of their attacks on the supply side ("dealers").
Yes, even in a legitimate market the regulations can fail and there are always loopholes and other problems. When the alternative is to hand piles of cash to violent gangs, even small improvements are worthwhile improvement.
Really, the people who still insist on full prohibition - that is, the people that are choosing to keep sending cash to gangs - are engaging in one of the nastier type of magical thinking. They make the assumption that simply by banning something, demand will magically change. In that view - where nobody should want drugs because they are illegal - it would indeed seem like the people "selfishly ignore the law an buy drugs" are funding various "bad" organizations. You see the same kind of magical thinking in other areas, too, such as "pro-life" groups. I suspect this type of attitude is derived from a Just World Hypothesis[2].
[1] If we can't cut off the supply side of the equation in prisons, we can't do it anywhere.
[2] http://en.wikipedia.org/wiki/Just-world_hypothesis