I just figured that Cerberus only wanted to still be secret in ME1.
Two years later, they're not concerned about that. They want talent to be aware that they're looking to recruit.
And ME2-ME3 time, they want as many people processed into their hivemind as possible, while still not requiring the mass numbers of military that the Alliance has.
I don't think they're secret (in terms of existence and presence) in the time after Sovereign's attack. Secretive, yes, but not secret. If anything, they want Shepard to brandish their logo everywhere: "If Cerberus is good enough for Commander Shepard, it's good enough for me!"
Cerberus = Reckless but calculated risk. Putting Shepard out there is a huge risk, but also a clear recruiting tool. To get enough of humanity and the rest of the galaxy to not necessarily see Cerberus as an automatic threat. And we see, even if mostly on the sidelines of the lore, that it worked. Many sleeper agents, many inside men, and seemingly contacts within the top of Salarian command.
Shepard only isn't immediately stopped at places like the Citadel and maybe Illium due to contrivances. Otherwise, the game wisely puts most events to take place in the middle of the lawless Terminus Systems or Krogan DMZ.