Assuming that Germany knew there was going to be an invasion, why didn't they deploy more naval assets such as U boats to pick off troop ships as they crossed the channel? I hear stories of how there were attacks on the eastern sea board but it would seem a better use would have been to patrol the channel.
By the time D-Day came around, the German navy was on the heavy defensive, and by the beginning of 1944, most German submarines rarely strayed far from the coast, and were largely confined to their ports - the last major action by the Kriegsmarine was in late 1943. One of the benefits of landing at Normandy was that there were not many major ports to house Kriegsmarine ships along the coast. The Germans had been led to believe that the attack would be at Calais, a major port and the closest point between the English and mainland European coasts. If the U-Boats were even able to leave their ports to aid in the defense, they would be positioned in a way to defend the Calais coast.
The Allies maintained a very powerful naval defense on both sides of the English Channel to prevent any U-Boats from attacking the vulnerable transport ships, meaning that U-Boats would not be able to hinder the invasion from the northeast. Additionally, transport had their own convoys so that any enemy ships that slipped through the blockade would be dealt with quickly.
TL;DR: Allies used deception and a massive naval presence to prevent U-Boat interference during the D-Day landings.
you would have thought they would have mined the channel as well
According to Herbert Werner in his book "iron coffins" all available UBoats were ordered to the channel to expend there torpedoes and the ram troop ships. He knew it was suicide and it would have been. I don't think his account is all that credible though. By that time ASDIC and air patrol would have easily detected any UBoat ballsy enough to try and sneak in. They could hardly get out of the bay of biscay at that point far less into the English Channel with a full invasion going on.