When a person is said to be confused, it means that he or she is intellectually muddled, unsure of what to think or do. When an idea or issue is confused, it is complicated and difficult to properly resolve. But when one thing is "confused with" another, this means that the person considering them (or their society/system of thought/etc) is confused, specifically that they believe the first thing is the same as the second, or that their identities are reversed. For example:

though they have different meanings, "flaunt" is sometimes confused with "flout."
(i.e., people are not certain which word to use)

Modern society often confuses love with sex.
(i.e., people think that love is all about sex, and if you've had sex you must be in love)