Flags and downvotes show up once you have enough karma (people have given you enough upvotes on your submissions and comments). You will see the down arrow below the up arrow once you get to that point, submissions don't get downvoted. "Flag" for submissions are on the comment page for the submission and underneath the submission title for the list pages (the main page, new page, etc.). "Flag" for comments is visible when you click the timestamp on a comment or the "reply" link (this provides a bit of friction, which is good for flagging as it's a more serious thing than downvoting).