We will be on the "Best of the Adriatic" tour this summer but are having trouble finding good air connections into Ljubljana and out of Dubrovnik. Have others from the Seattle area found good flights? We can also use the Vancouver, BC airport as we live north of Seattle.
I didn't go on a tour to Croatia (went independently instead) but I realized it was quite expensive and not straightforward to get to, even from where I live. So what you're experiencing is normal. Croatia is a much smaller market than other European countries and Dubrovnik is downright tiny, so it's not competitive to fly into and out of there. I ended up flying to/from Split via Frankfurt on a Lufthansa/Croatia Airlines ticket, and I made Split a part of my Bosnia and Croatia itinerary. It was easy to get form Split to Dubrovnik and vice versa via a modern, inexpensive bus.
If you can get to Venice easily and affordably, you can get to Ljubljana in about 2.5 hours directly from the Venice airport via DRD or GoOpti.
If you can get decent flights home out of Venice or Zagreb, there are more direct flights now between Dubrovnik and Venice.
Alternately, try booking separate tickets: get a direct flight from Seattle to Amsterdam, Paris, Frankfurt, etc. and connect on your own to Ljubljana; this will probably be easier on the inbound (arrive early in Europe after flying overnight) to do in the same day but on the way home you might need to stage a final night somewhere.
I use Google Flights to check for the obvious flights and book directly with the airlines if at all possible and avoid "middlemen" which can just complicate things later if there's a delay or change. Some people recommend Skyscanner, which probably will give you more options (or at least ideas) .
There is both bus and rail service between Zagreb and Ljubljana, and the trip doesn't take too long, so flying into Zagreb would be an option. Whether that will be any easier for you than Ljubljana, I do not know, but I was able to fly home to Washington DC from Zagreb in 2015 with just one change of planes (either Amsterdam or Frankfurt).
To book all on one ticket for each direction (and possibly also book as one-way tickets) try going directly to the web sites for Condor (I saw Dubrovnik-Seattle with one connection at Frankfurt) and/or Norwegian (Dubrovnik-Seattle via London Gatwick). Air France also seems to have options with one change at Paris CDG that might only be bookable by phone. I don't see much direct service between Dubrovnik and Amsterdam (only the independent EasyJet) making Amsterdam a less workable connection point.
I am on this tour in late spring, also coming from Seattle. I am, however, spending time in Prague first which changes my flight needs. Previous posters have mentioned Condor, and that is who I ended up booking with. I was having trouble getting a good flight out of Dubrovnik, so I'm going to Zagreb the day after the tour ends and flying out of there. I ended up with an open jaw flight, into Prague and out of Zagreb with a layover in Frankfurt each way. Condor offered the cheapest and most convenient flights by far, booking direct from their website. They might end up being your best option also.
I'm definitely keeping an eye on Condor for future flights. We have direct Condor flights from Portland now (not every day), and Alaska Airlines is a partner, so I can use my Alaska miles for Condor flights - as cheap as 25K miles one way for the direct flight. I used to take the Delta direct flight from/to PDX to Amsterdam when Alaska and Delta were partners but that partnership has ended, unfortunately. So far, I haven't found a Condor award flight that has worked for me, but someday I'm sure one will!