Command throws don't really work if the person is pressing buttons when they wake up. In my experiences, a lot of people online do this, and don't really allow themselves to be conditioned to stop pressing buttons on wakeup.
For bee and other characters that have really low profile low attacks (wolf, bulleta) you can step back a bit on wakeup and press st.hk. This goes over those lows. I use it in bee/wolf matchup a lot but haven't really found a use for it in other matchups.
For air to air, try to do air chains starting with j.lk and going to mp, mk, hp, hk depending on your distance to the corner. A lot of times, j.lk will stuff someone's air to air attempt. From there, you have to think about what they're going to do when they land from the air reset. You can command throw, dash j.mk or mp, or go for a low. If you think they're going to jump out, bust them up with st.mk or close st.hk.
I use j.fp a lot and I get a lot of success with it.