I am personally of the opinion that Christian churches ought to meet in homes rather than special buildings. That is how the earliest Christians met.
There is an article here:
How to have a participatory house church meeting (PDF)
This talks about some of the issues in hosting house churches. It points out that those hosting a house church meeting should lay down some house rules, which can include a rule about removing shoes.
Another article on house churches makes the same point; that it is fine for the host family to ask those attending to remove their shoes.
A family that are gracious enough to allow church meetings in their home should not have to suffer their carpets to be ruined or to have to do twice as much cleaning as everybody else. Those attending should show the respect of removing their shoes.