What does it mean that ripples are destroyed? I learn that, whether involving the transaction fees, or in some other cases, ripples can be destroyed. 

What does it mean?

If I was charged a fee, does that mean that nobody got that fee as a corresponding increase of their holdings in XRPs?

Or does it mean that there is no record of it anywhere except in my retina vision cells seeing 0.xxx less in my account and somebody else seeing more?
Nobody gets that fee, as simple as that.

To protect the XRP Ledger from being disrupted by spam and denial-of-service attacks, each transaction must destroy a small amount of XRP. This transaction cost is designed to increase along with the load on the network, making it very expensive to deliberately or inadvertently overload the network.
Every transaction must specify how much XRP to destroy to pay the transaction cost.

See the Ripple Developer Center for further details.