House has multiple political meanings
'House' as in "The United States House of Representatives" refers to a chamber of a governing body, that is, a room in which people meet to do a thing, and by extension the body that there convenes for official business.
Other examples would be the UK's 'House of Lords' and 'House of Commons', from which the US House descends, and who have actual official names separate from the much more commonly used names for the chambers in which they are held (e.g. the House of Lords is actually "The Right Honourable the Lords Spiritual and Temporal of the United Kingdom of Great Britain and Northern Ireland in Parliament Assembled" at present).
That kind of House, then, is appropriate in a RPG setting for an officially recognized typically legislative body composed of members who all get together in one set place periodically, deliberate, and vote on stuff. While the members of these kinds of Houses might be corrupt, the House itself is generally thought of as on the up-and-up when used this way-- you invoke ideas of jurisprudence, rule by the people (or at least the wealthy elite), healthy debate, freedom, etc. The negative tones invoked by this sort of House are bureaucratic sluggishness, a disconnect from the reality of the nation, political duplicity, etc.
The other usage of 'House' is older, and has to do with actual family lines rather than a particular place of business. An example of this second kind would be the Gens Valeria of Ancient Rome, considered one of the Great Houses of that country. You can see a list of other Patrician gentes here.
This sort of House is still a political entity, but not usually an official one and even less any sort of official governing body. Instead it is a grouping of allegiance, not function, and denotes a network of extended relationships and resources much in the same way as a guild, but organized explicitly by family line. This sort of House influences politics and governance, rather than being the government, at least outside its extended familial jurisdiction, and it takes its designation traditionally as a postfix adjective (i.e. 'House Stark' rather than 'Stark House').
Positively, it invokes ideas of grandeur, aristocracy, loyalty, wealth, long and storied histories, tradition and Culture, etc. Negatively, it invokes ideas of classism, racism, corruption, a lack of social mobility, political duplicity, cloak-and-dagger politics, etc.
Both of them are completely acceptable political divisions in an RPG, medieval fantasy or otherwise, but be aware they are different and don't equivocate them when discussing a setting or reading a campaign book: one influences the official government from within it, and the other is the official government (or, rather, a part of it).