score:7
Well these search engines provide you the flight itineraries (and if you have tried many sites chances are you found the best connections already).
However as you mention a combination of direct flights + ground travel might be advantageous. A good site to check your options is Rome2Rio. Here are their results for a search from Rome to Baltimore. That gives you a cost and time estimate for alternative options, but note that results are not date specific, i.e. for each of those you will have to manually search the connection for your travel dates.
In this case one alternative to connecting flights to Baltimore is flying into Washington Dulles airport and taking a train. The time saved compared to the shortest connecting flights is in the minutes so I guess your advantage would be in terms of price, if so. Note also that you would be purchasing two different tickets (flight + train) so your connection might not be guaranteed (and you have to haul luggage), while with connecting flights on a single ticket in the case of delay the airline is responsible for ultimately getting you to Baltimore.
Upvote:5
There are airlines whose flights are not in the search engines. I found a number of them while planning trips in the Pacific. Since you have starting and ending airports in mind, the website of the airport itself will tell you what airlines fly from it. You can then check their websites to see if you can find flights that are not in the big search engines.
In my experience, if you can find acceptable flights between A and B, there are not other, better, cheaper, less-stops flights between A and B hiding out there with other airlines. You get out of the big services and into the web site of the little airline in cases where the little airline is the only one who flies that route, and they don't want to be in the services (I think it costs them money.) So if you need to fly from Tahiti to Hiva Oa you'll need the Air Tahiti site. Flying from a US city to a large European city, not so much.