So far this is what I've been able to find. I still believe this has little to do with the federal budget, and should not be a part of this bill.
Under pressure from ranching interests in Montana and Idaho, as well as anti-wolf zealots in those states, Reid and Obama agreed to accept an amendment from Montana Democrat Jon Tester mandating the removal of grey wolves in Idaho and Montana from the endangered species list. For Obama, at least, the move isn't surprising: his administration backed the Bush administration's delisting of wolves even though it would allow the two massive states to cut wolf populations to as few as 450 individuals between them.
http://www.huffingtonpost.com/glenn-hurowitz/endangered-wolves-sacrifi_b_847673.html Sportsmen and ranchers, who make up a powerful constituency in Western states, have strongly advocated de-listing wolves and grizzlies, saying the predators are diminishing herds of big-game animals such as elk and are preying on livestock.
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De-listing means states would assume management of the estimated 1,700 wolves in the Northern Rockies - about 1,000 more than the federal recovery goal for the species.
http://www.washingtonpost.com/wp-dyn/content/article/2010/12/04/AR2010120403767.html Montana hunters appear to have been more successful in their bid to influence the legislation.
Senator Jon Tester, Democrat of Montana, said the budget bill included his proposal to remove gray wolves in Montana and Idaho from the federal list of endangered species. This would enable the two states to manage their wolf populations and to allow hunting of the animals if they choose.
“This wolf fix isn’t about one party’s agenda,” Mr. Tester said. “It’s about what’s right for Montana and the West.”
Senator Max Baucus, Democrat of Montana and chairman of the Finance Committee, had urged Mr. Obama to remove the gray wolf from the list as part of any budget agreement.
“Montanans don’t need D.C. bureaucrats telling us how to manage wolves in our state,” Mr. Baucus said.
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Montana officials want to conduct a regulated hunt of wolves, which prey on elk and other big game in the western part of the state.
http://www.nytimes.com/2011/04/11/us/11budget.html Ranchers have been compensated for livestock losses in the past by Defenders, but changes in compensation are being considered by the state (at least in Oregon), so Defenders has discontinued payments.
http://oregoncapitolnews.com/blog/2011/04/06/compensation-for-losses-caused-by-wolves-hangs-in-the-balance/Idaho Gov. Butch Otter is asking the head of the U.S. Department of the Interior to allow a wolf hunt this year and to have federal money pay for the cost of managing wolves in Idaho.
Otter sent a proposed memorandum of agreement (MOA) to Interior Secretary Ken Salazar outlining how the state and federal government would work together on wolves. The state lost its authority to manage wolves in an Aug. 5 court decision that put gray wolves back on the endangered species list.
In a letter attached to the new MOA, Otter told Salazar that delisting wolves remains a goal, but that until then, the federal government should cover the costs of managing wolves.
http://www.idahoreporter.com/2010/otters-latest-wolf-letter-to-feds-asks-for-hunting-less-cost-to-sportsmen/ The only budget issue I was able to find was this article, but I was not able to find any reference to what actual savings would be. Obviously any costs to manage wolf populations will be shifted to the states, which is part of the reason for removing the wolf from federal protection. The states don't have the legal option to manage federally protected species. I believe the main reason is by removing the wolf from federal protection, it gives the states the right to do what they want with their wolf populations. For some states the costs I would think would be very minimal, as there would be little actual environmentally friendly management of the populations by the state. Instead, the populations would be decimated by hunting, trapping, etc.
Minnesota officials were stunned to learn this week that among budget cuts made recently by Congress was funding for the federal wolf-control program in Minnesota.
The program, under which federal trappers trap and kill wolves that attack or threaten livestock and pets, has been eliminated. Federal trappers were on the job Tuesday, but could be pulled out of the field at any time, officials said.
That would essentially eliminate wolf management in the state because the wolf remains protected under the federal Endangered Species Act. The state Department of Natural Resources can't legally deal with problem wolves.
http://www.startribune.com/sports/outdoors/119712379.html 
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