I would say it is no bad thing for an agent to be involved in any well paid work. Your agent has a tool-kit which you probably lack: (s)he has damn good legal representation, can make sure you don't get messed around or bullied and, ultimately, that you get paid.
This takes an awful lot of anxiety out of the contractual process for you - and leaves you free to concentrate on what you do best - acting - without the personality clashes that can result from trying to negotiate fair treatment, and timely payment, yourself.
From the agents' point of view, it can save them the potential embarrassment of discovering that clients they submitted for something have actually been submitted by a third, independent, party (ie., another agent or web-agency).
It could also compensate them for any long periods when you are unavailable to take up the jobs they are hunting down for you because you are otherwise employed.
That said, many good agents do not often insist on collecting payment for jobs they have not negotiated on your behalf. The contractual clause is there, just in case, to help discourage clients from taking the piss.
It is also common for agents to take a reduced commission for work you have found yourself (say, 10% instead of 15%). Ask your prospective agent if this is the case.
It does seem a little greedy to demand, say, 20% across the board, even for work you have negotiated yourself - and there are certainly better agents out there (You Management - a new agency who claim to be run by, and for, working actors - ask for 10% for any jobs they find you, and 5% for work you find yourself).
For my part, bitter experience of losing pay or rights has led me to realise that it's worth having a good agent even if you do find most of your work yourself. When there is pay involved, I usually offer it to my agent to handle. They appreciate the gesture. Sometimes, they decline (in which case no percentage). But, for larger amounts, they'll take on the negotiation - and I am left with the reassurance that the business end will be handled skilfully and not cause me any unneeded stress. If you are sending work in the direction of your agent, they will see you as committed, and be all the more motivated to find work for you.