Same reason I do the same job as the ramp controllers in United's G-tower here at SFO and get paid half as much. They work for United, I work for a contractor that works for United. Contracted work in the airline industry will never pay as well as working for a mainline company. The whole point of airlines contracting out is to save money. While the airline itself doesn't dictate the contracted payrates, the contractor has to stay competitive and will pay as little as they can get away with.
Back to your example, let me give you a little background on Republic's 190s vs. JetBlue 190s. Republic first got those 190s to fly as Midwest Connect out of MKE, as a contractor for Midwest Airlines just like Skyway and Skywest had done. Republic's holding company bought Midwest and Frontier Airlines, merged them together dropping the Midwest brand, and then painted most of them up in Frontier colors(AFAIK one is still in Midwest Colors to this day, because they're classy like that) and started flying them on Frontier routes. While the planes said Frontier, and they were owned by the same holding company, Republic still ran the 190s as "Frontier operated by Republic", Republic hence remained a contractor, and the pilots were paid accordingly. Frontier was then sold off, and Republic stopped flying for them all together. Now, those same 190s are being flown for Caesars Casino's strictly doing charter work, and again, contracted. Republic has never sold tickets on those 190s as Republic Airlines and has only flown them where their partners wanted the planes flown.
JetBlue bought the 190s to fly in its own route network and flies them where they want when they want, and pay reflects that. But even so, JetBlue is an LCC that usually will be cheaper than US Airways, and thus US Airways is able to pay more for its mainline 190 pilots.
See the difference? I don't fly 121 yet, but my advice to you is never get too comfortable at a contracted company in any line of work. Get in, get experience, then get out. And its all about the company, not the airframe.