But I agree, supporting the network with only 0.0001 fee won't make them lose a lot 
True, but the 100-mike (0.0001-BTC) fee will also not support the network much, nor does it cost the miner much to include the transaction.
These "huge" transactions don't take up any more resources than simple transactions of far smaller amounts. The lion's share of the costs are borne by the sender in the form of risk as they may send to the wrong address or reveal sensitive information while creating/signing/broadcasting the transaction.
Just one 0.0001 fee won't do much, that's right.
If a block contains 1000+ transactions, the fees can add up and form a decent amount.
For example, block 333920 has 1071 transactions. Total generated fee amount is 0.17766577 BTC
