Well, the market for MSSQL on Linux would not be MySQL or postgres. They are clearly targeting Oracle DB, Sybase and others here, which are designed to meet enterprise level requirements, e.g. for the outsourcing business, DBaaS, financial services or government institutions. It's pretty obvious since Red Hat is involved in the deal, and I bet IBM will be the first big customer (for their zSeries). Actually it could help in the regular daily business too, because I grew a bit tired of converting terabytes of MSSQL databases and T-SQL scripts to PL/SQL and Oracle DB. That's a job I definitely don't want to do as a System Engineer and I would happily deploy MSSQL instead and simply hand it over to the customer's DBA.
If Linux or Windows is the stronger system... the customer who pays for the service doesn't care, except if he wants his own applications to run. That may be important for the $99/year customers of Joe Webhoster, but those customers will never pay extra money for clustered DB services or "Big Data" anyway.