Historically most banks have charged $1-$2 for an e-transfer (often with a limited number of free transfers per month, or a different type of chequing account one can sign up for to get free transfers), though it seems prices have been dropping in the past few years. Apparently the Bank of Montreal removed e-transfer fees on personal accounts a year or two ago.
So there's definitely still overhead that can make small transfers infeasible, but it's getting better.
CIBC has done the same. TD charges only $0.50 on the most basic plan and it is free on other plans. Simplii (née PC Financial) has always had free Interac e-Transfers. Interac fees have vanished or are vanishing for most people. The daily and weekly maximums are still an issue though ($3k and $10k at most banks usually).
So there's definitely still overhead that can make small transfers infeasible, but it's getting better.