Okay... to be honest and sincere for a moment...
I'm not a religious person by any definition; I'd consider myself an agnostic at best. Plus, in the Finnish language the phrase "You'll be in my prayers" or "Sendin' up prayers" just doesn't work in every-day parlance, unless you're a Pentecostal, born again or of some other conservative denomination that considers the modern way of life sinful, tries to resurrect the dead and/or treats vaginas like clown cars.
That being said, I have some foreign friends (Halforumites included) who have in recent months used that expression on me. I don't take offence from that, nor do I mock them for saying so. Like one such friend said today, it's something you say when you mean the person is in their thoughts, that you wish all the best for them, even if you're not religious yourself. It is a show of sympathy and solidarity, something you say to show you care for that person.
Does it physically help? There we go into the realm of how much of medicine is actually psychosomatic, dependant on how positive your personal outlook is to your situation. But it's nice to hear people care and wish for you to get better.
That's my personal take on the whole thing. You want to get angry at "social noise" like that? Go right ahead, no skin off my nose...