No, a Flying type Pokemon cannot be Poisoned if it uses Roost while a layer of Toxic Spikes is set up. There is another way around this though. Lets say your Nidoking set up Toxic Spikes on your opponent, and here your send out a Dusknoir after you set up and use Gravity, then if a Flying type Pokemon enters, they will get inflicted with Poison.
This goes for Toxic Spikes+Crobat as well. I mean that if a Poison type enters while Toxic Spikes are up, they go away. If Crobat uses Roost with Toxic Spikes are up, the Entry Hazard will not go away, but you can use the Gravity Trick with Crobat to get rid of them.