An unencrypted private key means if somebody can access your computer they will have access to your private key and your funds. If for some reason your private key is online, ie if you send it to yourself with an email, it can potentially be compromised.
To use some of the functionality of MyEtherWallet you need to decrypt your private key, for example if you want to send a transaction. That should be safe if you do that operation in a computer you trust it is not compromised.
If you have downloaded an unencrypted copy of the private key then you should follow a guide to securely dispose of such copy. For example this guide from Electronic Frontier Fundation How to: Delete Your Data Securely on Windows, they have other articles for other OS.
If you think that your private key might have been compromised it is best to generate a new private in a secure computer key and move your funds to the new address. Also if you have an important amount you can consider a hardware wallet.