Is it ok to give my 3 year old son some decongestant with amoxicillin?

No, there is a warning by the FDA that a decongestant is not to be used in children under 6. It will probably even say on the package. Decongestants contain ingredients like pseudo ephedrine and benedryl, which can cause dangerous low blood pressure in children that young and they cannot communicate that to you at a young age. It can also cause confusion, delirium and heart palpitations...can also damage the kidneys. Please your child will be ok if they have a flu or cold, our bodies were made to fight them, I know it's hard having an upset/ sick child but giving them these meds just so you can feel better is not the best option.
I commend you on at least asking this question, better to be safe than sorry.