> Why is this an issue?
Because, as opposed to the more adversarial nature of laws, regulations can be passed unilaterally, or by executive order. This makes for rules which may or may not be good, but are definitely expediant. I subscribe to Thoreau's opinion on the matter, but in the case of executive order, agencies tend to skip over or completely ignore the response for public commentary, which is yet another way to short-circuit the process.
> Agency rulings can still be challenged in court
Sure, but agency rulings, in order to be challenged, must first do harm, for without harm there is no standing. For everyone who has gripes with the idea of suing a large corporation, I would agree that those gripes are justified, and further posit that the federal government is the largest corporation of them all. It is hence impractical for a small or even medium company in most cases to fund a successful challenge to a constitutional infringement, and as the limitation of constitutional rights is considered an irreparable injury, it seems that we do it in fairly broad scale far too routinely for my liking.
Beyond all of the above, there's a very good argument, specifically due to the increasingly oligarchical nature of our government that those regulations which are crafted at the behest of the large companies as competitive advantage to smaller companies are exceedingly unlikely to be challenged at all, much less overturned.