I am looking for a hotel search engine for rural areas

You may like to check out Mapov.com.

It's a map-based Search Engine for Hotels and covers rural areas as well as cities. Because it's based on a map you can discover hotels in really tucked away places and get a good feel for the area.

It also shows the lowest prices from 7 of the world's top providers!

(Full disclosure: I currently work with the Mapov team)

I don't know if France is in the Southern Europe you target, nor if you are open to other types of accommodation than hotel.

However, there is an organisation in France that references place rentals for leisure. There are mostly bed&breakfast and cottages. It is usually quite friendly and most of the time in the middle of nowhere. Their targeted audience is actually people looking for a "City break" or "Charming place", quite close to your bucolic holiday. There is probably not any possibility to search how close the airport is though. This is called Gites de France.

As I quoted in this answer, one style of accommodation in some countries are the homes owned by the International Friends of Nature. This seems to be mostly active in German and English speaking countries, but not exclusively. Those are very bucolic accommodations. You might have to hike quite a bit from the nearest bus-stop or car-park! They are typically pretty low-budget and if you expect room service and a minibar you will be disappointed. If you search Google Images you will find some incredibly stunning locations.

Warning: you might risk making friends at a Naturfreundehaus!

They have a search engine for their accommodation at www.naturfreunde-haeuser.net. In the top-right you can switch to English by clicking on "Deutsch". Their interface translation seems incomplete, but should be good enough to get on your way.

For example, with this search engine (by country and region), I find:

• 419 places in Germany
• 12 places in Finland
• 4 places in the USA (all in California)

They might have some bias as to the homes included in the system (not sure).

I am not aware of a specific search engine that would allow this. The condition that secluded and quite places don't go together with those masses of tourists that would support the business models of the different aggregator services like booking.com, etc.

What works for me though is to use Google maps to find accommodation in rural places. The steps involved are as follows:

1. Identify the region you would like to visit. (e.g. Monshau)
2. Set the range you are willing to include in your search (To stick with Monshau enlarge the map to include Aachen and Stavelot).
3. Identify the name of your preferred type of accomodation in the local language (again in the Monshau example being either Ferienhaus (German) or Chambre d'hotes/Gites(French)
4. Type in either gite/ferienhause or both in the just enlarge area in google maps and the different accommodation options will pop up.
5. Contact the different options.

The most difficult part might be contacting the person offering the accommodation. Not everybody is fluent in English, but then this feature might support the "inaccessibility" of a region that makes it bucolic (like Mark this is a new word for me).

In France you want to search for "Gites", "Chambre d'hotes", "Tourisme Rural". In German so far I have only identified "Ferienhaus" (I would appreciate other synonyms). In Italian you could search for "Agriturismo".