The download folder can get messy fast, and for the most part, you won't be really needing its contents more than once.
Open a terminal and type
crontab -e
Then add the following line in the editor that pops up
* * * * * find Downloads/* -ctime +5 -exec rm -rf {} \; > /dev/null 2> /dev/null
This will delete all files in the downloads folder older than 5 days.
This is a power tool, use with care! Make sure you remember to move your downloads elsewhere in time. The upside is you will always find your latest downloads with ease. 5 days worked great for me, but replace +5 to a different number of days if you like.
I love linux. You can just make it do stuff your way with one liners.