In reference to Cain being the son of Adam and Eve, it IS clear that Cain was Adam's son. When it said that he "knew" Eve, it meant that he made love to her. Here are some alternate translations to clarify.
(NIV) - 1 Adam made love to his wife Eve, and she became pregnant and gave birth to Cain. She said, “With the help of the LORD I have brought forth[c] a man.” 2 Later she gave birth to his brother Abel. Now Abel kept flocks, and Cain worked the soil.
(New American Standard Bible) - 1Now the man had relations with his wife Eve, and she conceived and gave birth to Cain, and she said, "I have gotten a manchild with the help of the LORD." 2Again, she gave birth to his brother Abel. And Abel was a keeper of flocks, but Cain was a tiller of the ground.
(New Living Translation) - 1 Now Adam had sexual relations with his wife, Eve, and she became pregnant. When she gave birth to Cain, she said, “With the Lord’s help, I have produced a man!” 2 Later she gave birth to his brother and named him Abel. When they grew up, Abel became a shepherd, while Cain cultivated the ground.
(Contemporary English Version) - 1Adam and Eve had a son. Then Eve said, "I'll name him Cain because I got him with the help of the LORD." 2Later she had another son and named him Abel. Abel became a sheep farmer, but Cain farmed the land.
(New Century Version) - 1 Adam had sexual relations with his wife Eve, and she became pregnant and gave birth to Cain. Eve said, "With the Lord's help, I have given birth to a man."2 After that, Eve gave birth to Cain's brother Abel. Abel took care of flocks, and Cain became a farmer.
So Cain does, indeed, belong to Adam and Eve. :)