Ubuntu Bitcoin-cli fee problem
The value of the transaction fee is not at all tied to the value being spent. It is entirely based upon the weight of a transaction as defined by BIP 141, which is based on the size of a transaction in bytes. To pay a lower fee, you need to make your transaction smaller by spending less inputs and creating less outputs. There is no way to spend fewer inputs except to not receive many low valued payments.

If you are receiving those payments by withdrawing from some service, then you should wait for your balance to be higher before withdrawing.