Surely it's the responsibility of the company to make sure that its service is available for all.
If you're talking about a private company, then no. If it's public transportation then yes.
You wouldn't expect a disabled person to pay extra because they're more of a hassle to transport.
Again, if it's a private company then yes, they have every right to charge more because disabled people cost more to transport. Money doesn't grow on trees.
If it's the govenment doing it, then the extra costs gets absorbed by the taxpayers.