President Obama's health care plan would use federal dollars to pay for abortions in at least three ways.
First, it contains Ben Nelson's so-called compromise amendment in which allows insurance plans purchased with federal subsidies to cover abortions. Nelson's amendment doesn't apply to the whole bill, so there are two other provisions that would allow direct federal funding of abortion.
The National Right to Life Committee notes that Obama's plan would provide $11 billion dollars for community health centers--$4 billion more than the original Senate bill--and there is no language preventing these funds from paying for abortions.
Third, the Senate bill allows for direct federal funding of abortions on Indian reservations.
All three of these measures were slipped into the Senate bill at the last minute in the manager's amendment. Ben Nelson admitted that the funding of abortions on Indian reservations was an oversight that would "have to be addressed in the conference." Except now there isn't going to be a conference--just a House vote on the Senate bill and some minor fiddling with the numbers through reconciliation with no significant changes to the abortion language.
Members of Congress liked to hide behind the fig leaf of Nelson's "segregation of funding" amendment to claim the bill banned abortion funding, but they can't make this claim regarding community health centers or Indian reservations.
The NRLC outlines more abortion-related problems in Obamacare here.