It is condescending, and an insult.

Suppose you enjoying watching football games. You then meet someone, who discovers this about you.

That person then arranges for you to be admitted into a psychiatric hospital, and schedules you to have regular sessions with a psychiatrist... all in the name of "helping" you.

That person may have legitimately wanted to be helpful, but the direct implication is that there's something wrong with you. You're broken, need help to be "fixed", or are generally just down on your luck and need a helping hand.

If you tell someone that you're a Christian, and the response is, "I'm so sorry. I'll see if I can arrange to get you some help with that.", wouldn't that be at least somewhat insulting?

That is what's conveyed to the atheist, and if she/he replies, "Thanks, and I'll think for you.", you'll now understand where the ire comes from. What else would you be praying about, other than requesting some aid (or harm) for this person?