It's about ... (major spoilers ahead)
... God. Little Joe is God.
Like God, He wants you to "breathe in" His essence.
He communicates with you telepathically or by altering your thoughts and swaying/ influencing your emotions.
He wants your utmost loyalty. This is a very important point.
He makes a group of people come together and think alike.
He wants you to respect and fight for Him.
There was nothing sinister about Little Joe at all... He was essentially seducing the people who took in His pollen. Think of the pollen as being His "sexual essence". If you think of it that way, ingestion of the pollen was a sexual act of union - He wanted a committed relationship in return.
Great movie! Gonna ponder this one for a while.