Airlines do not charge more for paper tickets but the trend is to discount E-tickets. If a travel agent charges for ticketing services, the fee is the same for paper or Electronic. Some travel agents are still not charging any fee's, others are charging as much as $25.00.
Airline commisson rates vary from country to country. Tickets sold from the US and Canada from/to anywhere in the world get 5% and are capped at $50 to $100. Not all airlines have caps or charge 5%. British Airways, National and Southwest still pay 10% with British only paying 5% on Business, first and concord. Commisson rates for many European agencies is currently at 5%-7%. In latin America the spread is from 7% to 15%. The only place I have seen zero commission is in Singapore, where Singapore Airlines has been testing a new net fare concept with some of their corporate travel agents.
In the future, excpect things to get very uneven with some airlines going to net fares, some trying to form dealerships, and others trying to find ways to go around the current CRS systems. This is a very complicated subject. The recent cut in commissions is most likely due to the airlines trying to off-set the higher fuel costs and to try to change the distribution chain.