Emphasizing in paper: italic or bold?
It's a matter of style: both bold and italic are typographically acceptable ways to emphasize part of your text, as are small caps, use of a different typeface or point size. (And, if you wonder: no, underlining is not considered good practice in modern printed text).

However, you are right that using bold is usually reserved for headings or very strong emphasis (think things like “Danger of electrocution — do not use under water” is an appliance user’s manual). The reason it is not commonly used inside running text is that it disrupts the overall level of gray of the page, drawing the eye from too far away: you want emphasis to make certain words stand out in the sentence, but you do not want the reader to skip directly to these words as soon as they set their eyes on the page.

There are, of course, always exceptions… like when you use bold (or color, or any other device that disrupt the grayness of the text), to emphasize a few stand-alone “take home messages” from a longer text, as I've done above!