All funds (money market, bond, mutual, etc) have fees associated with an "expense ratio". That is the amount of money spent to keep the fund going and comes out of your money in the fund.
Some funds also have loads. Don't buy loaded funds. Fidelity is great and their funds don't have loads.
Many funds have fees for short-term holding, so if you buy and sell in a short time (say 90 days) there is an associated fee. All of this information is very clear on the fidelity fund information page.

For an IRA investment index fund, you should look to pay very low expense ratio, Fidelity has both domestic and international index funds with no load and .1% expense ratios. FSTMX is a wilshire 5000 index fund with a .1% expense ratio, and is my recommendation for a domestic index fund. There is a 10K minimum for retirement accounts though. FSMKS is the S&P 500 fidelity index fund and is also .1% expense with a 10K minimum.
I can tell you from experience that Fidelity is fantastic about low/no fees. I rolled my Roth IRA over from the money grubbing bastards at Morgan Stanley and haven't looked back since. I've literally never paid a cent for my Fidelity IRA (aside from expense ratios for the funds). I wasn't charged opening the account, I wasn't charged to fund the account via bank transfer, and I've never paid any fees associated with "account maintenence" or investing in funds (not only does fidelity have many of it's own fantastic funds, but they are partnered with many others with "No Transaction Fee" or NTF funds.
I'm not sure what you're specifically talking about in your post, but Fidelity is very honest about fees. Vanguard is no different, they are another great investment house with low/no feed (called "discount brokerages").
Whether you choose to go with Fidelity or Vanguard is up to you, but I highly highly recommend Fidelity.