The question is pretty general.
Respected, "by whom?"
By the cretins who post hate on the Jests and Indy Boards and elsewhere? By the mediots who turned Spygate into a Cottage Industry? No. Never. If they ever were.
By the vast majority of fans outside of New England who used to admire them for winning (even if they were pulling against them, like the old Cowboys or the Yankees) but are now either negative or ambivalent about the Patriots? Yes, but, fairly or unfairly, it will take a while and, fairly or unfairly, I don't think their respect will return as long as BB is coach. The latter is terribly unfair and sad, but I think it is true.
Respected, "for what?" For being an outstanding Football team? Even ESPN has ranked them Number 1 in the pre-Season Power rankings. Yes.
For being a (the!) model NFL Franchise? Eventually, but it will take a few years and, sadly, the departure of the guy who had as much to do with building that franchise as anyone.