I'm not in the industry, but at a guess....
For big groups, each route has to pay a small contribution to the group's CEO salary (which is probably 10 times the salary of the small owner,) plus there is the cost of HR departments (rhe small owner may do his own HR), H&S etc etc likewise.
Also, it may be that a small operator has 5 routes, and overall the company makes a small profit, but the owner doesn't really know how much each route makes because the buses and staff inter-work. However, a large company will want to know the profitability of each route, and has staff and software to access this. Lastly, the profit expectations of large groups is higher than for the small independent operator. Against this though, big companies can probably get advantageous fuel prices, cost of spares, and new bus prices/lease deals.
Also, take the example of the 5 routes above. If the franchise splits these routes into different lots, then the small owner will not know how much to bid for each of these routes, and has no real experience of costing each route, so is at an immediate disadvantage to the big boys.