A tale of two bunnies...

No, cottontail rabbits are probably not in danger of extinction.  Although if expanding the species is important, it might be a good idea to use incentives to encourage more landowners to make habitat for the New England subspecies.  If the endangered species act is used as a weapon against land owners, you will have more incentive to go out and make sure there are none of those rabbits on your property.

When there were more farms, species such as the New England cottontail rabbit benefitted.  New England before the Europeans came was mostly forest (although there was some clearing done by Native Americans).  21st century New England is reverting back to mostly forest (like it used to be).  So there is less manmade rabbit habitat.  The subspecies in New England is being replaced in some of its former range by the eastern cottontail subspecies which seems to do better in suburban habitat.  They look almost identical (except the New England subspecies seems to have shorter darker ears and is a bit smaller).  They can't seem to successfully interbreed which does suggest they are separate species.