Why did the Queen name her son and heir “Charles”? After King Charles I and King Charles II?

Maybe she likes it.

The Queen is a dog person.

Why not?  It's a good name.  It's my husband's name.

Why not?  Charles II has a popular reputation as the Restoration King and the "Merry Monarch".  He's not viewed negatively.  His reign was something of a cultural renaissance for the country, even despite the plague and the fire -- which were not his fault, obviously.

Virtually any traditional name they could have chosen would have had SOME negative associations.

I doubt Charles will choose a different name as a regnal name. He's been known as Charles for so long that no one will ever think of him as anything else.

She didn't Charles is a name that runs in the Royal Family.

But his name has nothing to do with King Charles I and King Charles II

King Charles I (the Martyr) is not the best namesake, but the "merrie monarch" King Charles II was feted in his time (but in Catherine of Braganza had a much more unpopular consort). Charles and Anne were popular Stuart names. It will be interesting to see if the Prince of Wales does change his name, but the chances of it being Arthur or Philip are remote and happily not something we'll have to worry about on this site.

Presumably it is a name his parents like. Monarchs rarely use their 'personal' name when they become king: Princess Alexandrina became Queen Victoria, Prince Albert (Bertie) became Edward VII, Prince David became Edward VIII etc. It is thought that Charles will become King George VII.