Yes I agree, that it is all too easy to play along with a metronome without playing in time with it. The thing is to listen carefully, and try to play so exactly in time that your note merges with the metronome beat. When you get it right the metronome sound can be heard to merge and may even vanish so that it seems to skip a beat. Then you have to do that on every beat.
To help with this musicians can use my Bounce Metronome Pro which has conductor visuals. With the bouncing ball, drum stick or conductor's baton, then you can see the exact moment of the beat before it happens - and play exactly along with it. That way you can also play rhythms with swing and other irregular beat patterns. You can use it for all sorts of rhythms including polyrhythms etc.
It's here:
Bounce Metronome Software
and comes with a free fully unlocked 30 day test drive.
I've got a page about staying in time with a metronome here:
How to sing and play in time
Screen shot of the drum stick visuals: Drum stick 3o4 metronome
Any comments or suggestions very welcome.
Robert