The only Anti Air you should be using against shotos like Ryu is St.mk.
No air throws?
I rarely use Air Throw on Ryu’s unless I find that they jump alot at close range (which is kind of stupid, imo). I personally try to bait them into making mistakes by getting close.
Bottom line, all of Guile’s normals serve as anti airs. Each one covers different ranges and angles. Get used to using all of his AA’s and not just cr.hp or flashkick. Learn which Anti Air is best at which range/spacing and go from there.
what stuffs his jump-in fierce? crhp does not work at all…if it does it trades…and its in his favor…
far st.mk = Shoto anti air.
(lowers Guile’s hurtbox while extending his hitbox up higher).
Eh, s.mk will still sometimes trade with his j.hp. I mean, shoto j.hp is GOOD! And, yah, while the damage is in his favor on a trade, the positioning is in Guile’s favor.
I’d rather take a trade than a full jump in combo. 
So how do you guys go about doing s.MK? I keep forgetting about it and when I use it I usually have charge on autopilot, so I get Back/forward/ medium kick which is diffr. any tips to get my s.MK AA game on point?
Just let go of the stick every now and then. Many times, I hear charge players state sitting on a charge all the time limits your game.
It’s natural that it’s hard to get into the habit of using st.mk. Just mind your range to the opponent. For characters with regular or lower jump arcs, keep st.mk pre-loaded in your mind whenever you stand at their jump-in range. Tell yourself, st.mk is the best chance you have of safely anti-airing the jump and believe in it.