Take it as they mean it.
"Bless you" is usually (bar the passive agressive "Bless" ) well meant.
"I'll pray for you" usually warrants "Fuck off" or, if time permits, "I'm apostate, so if you pray for me, by your own rules, you are damning your own soul." With verse. Something in Matthew IIRC.

My first born used to own a dog that sneezed at you when mad at you instead of barking... so you may still look cute and not rude. I just thank them with nothing behind it.

I tell them I'm not religious or just ignore them.

tell them bless you came from the bubonic plague . the first sign was a cold so the priest would give you your last rites there and then . bless you !

If they mean well I just say "thanks" in a non excited manner and typically the conversation is over or subject is changed.

Since you mention that nice people do this, a hearty sincere thank you will suffice, accompanied by a smile, followed by a quick exit stage left.

I always say, "Thank you" because It's meant kindly. When someone else sneezes, I say "Geshundeit!" because it sounds like a sneeze.

I don't even try. I'm not being rude, they are.

Although I do have a tendency to sneeze repeatedly sometimes and my wife reflexively says "God Bless You" multiple times in sequence and it gets me really just pissed off. She can't help herself.

It's fine. I just say thank you. That's the least offensive thing they can possibly do.

Smile and thank them

I just say "thank you," and pretend they were only sending me positive energy.