No they weren't. The Luftwaffe did not maintain standing patrols over such facilities, it had many other things, including its own airfields, to defend.
By the BoB the RAF was already resorting to bombing by night, with the exception of the Blenheim force which still operated largely by day. Bomber Command was committed to too many targets. Oil, communications and the Ruhr were still the primary targets, though docks and other industrial infrastructure were to be attacked too. Luftwaffe airfields in the Low Countries and France became targets in June as well. The first attack on invasion barges,by 33 Blenheims, was on 3rd July. These were attacked near Rotterdam as they were brought up the Rhine. On the night of 21/22 July even the venerable Battles of Nos. 103 and 150 Squadrons were thrown in against barges in Dutch ports, their first operation since transfer to Bomber Command. The largest attack on invasion ports came on the night of 15/16 September when 155 aircraft attacked various Channel ports. The operations against the invasion ports were frequent and the last major effort was on the night of 12/13 October at atime when the threat of invasion was fast receding.
From 26th June to 13 October Bomber Command flew 1,885 daylight sorties and 8,804 night time sorties. Losses by day amounted to 3.5% from all causes, by night 2.3%. Given the innacuracy of bombing at this time it will be debated just how much damage the bombers did to the invasion fleets. It is often forgotten that the Royal Navy also mounted operations against them, regularly shelling the ports and assembled barges with considerably more accuracy.
Cheers
Steve