Looks like you will need to make a connection through Dublin to get to Kerry. You could do the direct flight on Loganair into Edinburgh and then book a Ryanair flight for Dublin onto Kerry. (Dublin and Kerry can be on one ticket). This means you will need to give yourself enough time to make the connection in Edinburgh. When you buy separate tickets on separate airlines, you will need to re-check your luggage. it is like getting on a brand new flight all over again. A word of caution, if your flight is late getting into Edinburgh and you miss the Dublin to Kerry flight, you will be responsible for re-booking a new flight. You are basically considered a No Show. Loganair has no responsibility beyond getting you to Edinburgh. Also, watch Ryanair's carry on-rules they are very strict. I would work it so I had lunch at Edinburgh airport. If you keep all this in mind, there is nothing wrong with getting separate tickets. The good news is Ryanair flights are pretty cheap.
(Alternatively, I believe Logan air will sell a ticket via Aberdeen into Dublin, but you still need to book a separate ticket to get to Kerry). But I would price it out. I think Ryanair will be the cheaper option.
Either way, your whole day will be spent traveling regardless of how you end up getting from point A to point B and C. I like the Dingle peninsula but Scotland has a lot to offer, and personally, I would stay in Scotland and do Ireland on another trip. You don't say how many days you have planned and that would factor into my decision.
