A sad state of affairs. In any system, whether it be security or quality control, there has to be a system based on redundancy, I know there were two checks in F3Gs case (checkin and gate) but if you used an automated checkin facility you may be reducing it to one or none.
For example in Zurich, which I travel from often, I always use the automated check in, I then proceed to passport control where my passport is checked but not my boarding pass. I then proceed to the gate where, and I'm only flying internationally from Zurich, my boarding card is enough to get me on the aircraft. Once I'm on the aircraft there have been no checks to see if I'm actually the person named on the boarding card.
In Strasbourg it's a different story completely. I'm nearly always in possession of a paper ticket where I can't use automated checkin so I go to the counter and checkin where my identity is always checked via my passport or my Carte Spécial (ID card), at security my boarding card is checked but not my identity. If I happen to be travelling to LGW then both my person and hand luggage are hand searched and this applies to everyone going to LGW and has been like that for a number of years. If I'm heading on a domestic or internal schengen flight then my ID card is checked against my boarding card at the gate, and it really is checked, they run their finger along my name on both items. Again, it's always been like that. If I'm travelling outside Schengen then I pass through passport control where my passport is checked against my boarding card and, get this, the police officer in the booth has a printout of passenger manifest of each flight (there are only about 4 non-schengen flights a day though) and he puts a neat tick by your name on the printout. My ID card and boarding pass are again properly checked at the gate.
Strasbourg is the exception and in my experience most gate agents in mainland europe don't check ID against boarding cards, though I should say there is normally a separate layer of security for those travelling to the UK and US where this does happen.