The side quests you've been completing for Rhys and Halen are infinitely repeatable side quests and do not directly progress the main story of the game. The Brotherhood of Steel quests leading up to the Molecular Level are as follows:
- Fire Support: Join the shootout at the Cambridge Police Station.
- Call to Arms: Follow Paladin Danse to ArcJet Systems.
- Semper Invicta: Accept your first quests as an official member of the Brotherhood of Steel.
- Shadow of Steel: Hitch a ride on an airship to get a promotion.
- Tour of Duty: It's orientation day at the Prydwen.
- Show No Mercy: It's time to hunt mutants.
Since you're already doing the side quests for Rhys and Halen you've likely already completed at least Fire Support and Call to Arms and if Danse is not talking to you then you're probably on Shadow of Steel.
For the Shadow of Steel mission you need to tune your Pip boy into the military frequency named AF95, which will then update your Pip boy with instructions to meet up with Paladin Danse on the roof of the Cambridge police station, to fly off to the Prydwen.