This objection is truly illogical: someone one who gets federal subsidies to open a small business might also smoke pot on the side. Does that mean the federal government is subsidizing his pot habit? More to the point, private insurers all cover abortion because (even though it is illegal to explicitly carry out this cost-benefit analysis) abortions are cheaper than prenatal care. Stupak's beef is with private insurers, not with the federal government.
On the reverse side of the coin, several Hispanic Democrats are threatening to bolt because illegal immigrants would be prohibited from buying private insurance in the federally-regulated exchanges. Similar to the abortion language, illegal immigrants can not get federal subsidies anyway. What the Senate bill does is that it prohibits private insurance companies from taking on illegal immigrants. The Senate bill is idiotic: it is like prohibiting Southwest Airlines from selling tickets to illegal immigrants. So, the Hispanic legislators do have a point. But such rules go against the best interest of the industries in question -- no industry wants to turn away customers who voluntary give it business. You can be sure that the law is not going to work.
The common thread to both the abortion and the immigration argument is that they imagine that the federal government can actually ban abortion coverage or ban coverage of illegal immigrants. The law tries to do one and not the other. But neither effort is going to work because insurance companies will make more money by covering abortion and by covering illegal immigrants. Both will go on regardless of whether health reform passes or not, and regardless of what the law says. Bart Stupak is fighting a losing battle and the Hispanic legislators are afraid of a phantom threat. Unfortunately, even though their fears are exactly contradictory, both these groups are "No" votes on health reform.