I don't understand the bolded bit. You don't have the choose the UA routing if you don't want to do so. If AC flies there than you can choose the AC flight (and not pay the baggage fee), no one is forcing you to choose the UA/US Airways/whoever flight. If AC doesn't fly there then, yes you do have to go with a partner airline (and pay their fees), but the alternative is no flight as all (since AC doesn't fly that routing).
I don't see what it unfair about this - AC is providing you a service by allowing you to book partner flights through AC.com rather than you having to search around to see which partners fly your routing (much like UA provides the service of allowing you to book AC or US Airways, etc. flights). The alternative is for AC to only show (and allow to be booked) AC flights, UA.ca to only allow UA flights, etc. This would would make life much more difficult to consumers than it is now.
For example, AC doesn't fly to Maui on the dates I want to go. So, if AC didn't allow me to book my flight on UA, I wouldn't be able to book my flight at all (without going to the UA website, where I'd be paying the baggage fee anyway).
If the websites were hiding who was actually operating the flights (and thus the fees), I would agree with you, but since they are not (at least UA and AC are not, I cannot speak to other websites), I don't see the problem at all. If you were to book on Expedia, for example, you pay whatever fees the airline you choose has, so you might have to make a choice between the flight times you want and the fees you'll have to pay (for example).