It is possible to have more than one plane travel between the same two airports in AirlineMogul.
However, it is not on the same route (as defined by the route ID number).
Say plane 1, flies from JFK to LGA with a frequency of once daily. If plane 1 has not more time, but you want another plane, plane 2, to fly JFK to LGA, you can do so (as long as you have enough slots), though the route number plane two has will be different.
Pros:
More money
Cons:
You may be able to make that money more efficiently by sending Plane 2 to another airport, say EWR.
(Yes I know that JFK, LGA and EWR are all really close to each other and to my knowledge not served directly from one another. Except JFK-EWR via helicopter.)