Under those stupid McCain-Feingold campaign finance laws passed in 2002...
it is illegal for a candidate to coordinate with a 527. If Bush is seen as coordinating with them by attacking the ad, then those of the Left will scream about him breaking the law (which he should've vetoed, IMO).
Those Swiftboat vets have the same 1st Amendment rights as anyone else. They were there and have a point of view that the mainstream media will never show unless the groundswell is overwhelming. So, they took a fully legal action under the law to get their message out.