It is as secure as any electronic system can be.  When Using the Online software, you do have to create your own UserID and Pwd and keep those complex and secure.  

Preparing manually on paper with the forms from the IRS website might be safer, as long as you trust the Post Office.

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Free?  Depends on what information you have to file.  with the "Free Edition" W-2 income only, and no itemized deductions or special credits and no investment income other than Interest and dividends you "Might" be able to use the Free version.

But for more complex tax returns where you are claiming special Credits,  Itemized deductions, or any stock sales or Mutual Fund Cap gains distributions or Self-employment income...then you'll end up in one of the pay-for-the-software versions.  IF you itemized Deduction last year and had a state refund, then you'll have to upgrade to one of the paid versions this year..That can happen even if you are using the Std Deduction this year.

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If your income is low enough, there is a "Free File" version that includes everything (this is not the same as TurboTax's "Free Edition" ....note the subtle name difference)    the "Free File" version is at this website  (IF you qualify to use it):

https://turbotax.intuit.com/taxfreedom/