An agent can be worth their weight in gold for a specialist itinerary such as a safari or lesser travelled countries, impossible to visit Nort Korea without using one.
Cheap hotel deals for stop overs are often best found through the airline, Emirates offer a wide range of packages for Dubai.
For heavy users such as companies, bulk discounts can be offered and agents have access to trade only offers.
However, it's not unknown for agents to steer customers towards packages which pay them the most commission. Low cost airlines often pay nothing and booking fees get tacked on if they are offered at all.
A well known chain was featured on a consumer program not too long ago and older non internet savvy customers ended up paying more than younger ones who had done their research online first.
Find the best deal you can and ask an agent if they can do better, you might get lucky if sales targets need to be met.