How do you mean, exactly? The thermae were quite hygenic. In fact, you were much more likely to get ill outside the baths than in it. They were fed by a constantly-flowing supply of water from an aqueduct, and the larger (Imperial) thermae had an army of slave attendants to keep them scrubbed, heated, supplied, and running smoothly. The large baths in Rome and the major cities were extremely opulent, paved with elaborate mosaics and adorned with expensive statuary and art. They were emblems of the Emperor's largess to the urban plebs, my point being: they weren't dirty, shabby operations.