Amsterdam is miles ahead in terms of infrastructure. This ranking dilutes the most important thing to get these results : good bike lancés everywhere with no discontinuity.
Disclaimer : I've built villes.plus, an open source automated evaluation of bike lanes. 100 points, compute itineraries in "secure" mode with Brouter between these points, count the % of secured km -> score.
Amsterdam tops at 8/10. Bordeaux is at 3/10, Nantes 2/10.