I'm inclined to support the government on this one.
Convention states that a government receives a majority on the committees. The current government may be a minority one, but it's a minority one that has the necessary votes to continue to function. Plus it's not as though the government is stacking the committees so that its MPs heavily outweigh Opposition MPs. The Brexit committee, admittedly decided upon prior to this vote, is fairly well-balanced.
It makes sense for a government to have a majority on the committees, however slim that majority may be within them. Otherwise the committees can act like a third chamber and absolutely wreck bills proposed by the Conservatives despite the fact that it is the Conservatives who have the support of the House to function as a government and not the other parties. If the Conservatives are to operate a minority government and pass its legislative agenda (which the House has decreed it has confidence in), then it should be allowed a slight majority on the committees.