It seems like to combine two or more tables, we can either use join or where. What are the advantages of one over the other?
You can't use WHERE to combine two tables. What you can do though is to write:
SELECT * FROM A, B
WHERE ...
The comma here is equivalent to writing:
SELECT *
FROM A
CROSS JOIN B
WHERE ...
Would you write that? No - because it's not what you mean at all. You don't want a cross join, you want an INNER JOIN. But when you write comma, you're saying CROSS JOIN and that's confusing.