The mines laid by Britain in the English Channel mentioned in the article are of particular interest as it describes them as "anti-submarine" mines. How does a mine know if it's contacted a submarine rather than a ship?
The English Channel was, most definitely, open to navigation by surface ships (even German ships) but definitely closed to submarines. So... did every man & his dog have a map showing where not to go? I'm pretty sure such a map wasn't captured by Germany. All they'd need to do is watch for a few days to see where ships went. Or was it simply that these mines were tethered in such a way that they remained submerged and, therefore, were only a threat to submerged units? This implies that a surfaced submarine would be able to pass over them without incident. Other than running the gauntlet of the RN, RAF and whatever coastal batteries were awake of course.
It is a matter of depth. The mines were placed low enough that surface ships would not trigger a detonation when passing over them.
Indeed subs could have travelled along the surface and been safe from the mines, but they'd have been very vulnerable to other things.