We know we've got a real problem when a phrase like that has become--at least in pop culture portrayals--a sign of condescension.
The majority of the time, it isn't...it is a sincerely-spoken phrase, out of genuine compassion for a person and whatever difficult or painful situation they may be going through. We know as well that prayer is also at times something like a weapon, a powerful force God allows us to take part in, against the forces of darkness. But sometimes, we choose to wield the wrong kind of power.
"Prayer" as an offensive weapon has been with us for thousands of years...a perversion of what should be a healing act. The parable of the Pharisee and the tax collector (Luke 18:9-14) is one of the clearest examples of this: the Pharisee gives a prayer of "thanks" that he is not like the sinful man sharing the room with him. In other words, in the act of prayer he is attempting to prop himself up at someone else's expense!
What right do we have to prop ourselves up at anyone else's expense, when we too are guilty--as C.S. Lewis put it (I paraphrase)--of high treason against the Almighty?
We might not express our inner hearts in public as blatantly as the Pharisee of the parable did, but when a Christian ends an argument with someone whose behavior or belief they disagree with with the words, "I'll pray for you," the tone is sometimes quite unkind. I know I've had it directed to me after expressing an opinion that someone disagreed with...and it very much struck me as an assertion of superiority rather than a blessing.
I don't think we should shy away from offering prayer. But I think we might do better to think of ourselves as prayer servants: when we undertake to pray for someone. It is no accident that we often kneel to pray...it is a humbling act. It is not a tool for stoking feelings of superiority, and conveying such an attitude towards others. When we do volunteer prayer, we need to make sure to do it lovingly, and with a servant's heart. Other times--and we should rely on the Holy Spirit for discernment here--it may be best to pray quietly.
But whatever we do, prayer should be an act of servitude. That does not stop it from being a powerful weapon against evil...indeed, it is by serving in accordance with God's ways that it really means something.
And with that as a guide, I believe we can pray in a manner that truly will heal hearts.