I get what you're saying about effective capacity, but absolute capacity would not be increased just by tolling it.
Where would all the drivers go that would be dissuaded from driving on the 401? Wilson-York Mills-Ellesmere? Sheppard? Lawrence? Finch? And if the 427, 400, 404/DVP are not tolled as well, then the on- and off-ramps for those highways could be a nightmare.
If the overall number of cars are reduced on Toronto roads (including the 401), that wouldn't necessarily be a good thing. A lot of those people don't have other good options. Driving often costs more than transit, but it saves time (even during rush hour) and makes long commutes feasible. IMO transit sucks so bad in Toronto that I just don't see that many people switching to transit from the 401 simply due to exorbitant 407-like tolls. They're more likely to switch to non-highway arterials. Given the location and importance of the 401, I assume the tolls on the 401 would have to be higher than the 407 just to achieve a minimum 85-90% speed limit from 6am to 8pm.