TT will ask you in what states you lived and in what states you worked. Where the company itself is located doesn't matter. Where you worked and lived does.

Since you were an employee you will have a W2 to enter when TT asks you about that.

If the W2 shows withholding in CA and you did not work in CA, you can probably file a non-resident CA return and get a refund. Often for small amounts people just let that go. You can check the CA tax website for the non-resident rules before paying for the CA state return in TT.

If you work remotely as an employee of a CA employer, you will not need to file a CA nonresident state income tax return related to this income. This is due to the fact that income in sourced to where the work in performed (FL) regardless of where the company is located (CA).

Since you will not have a CA state income tax filing, just check that you selected "no" to " Did you make money in any other states?" under the Personal Information section in TurboTax (see screenshots)

If you have any CA withholdings on your W-2, then in order to get the full refund of your CA state income tax withholdings, you will need to file a nonresident CA return but report zero "0" income from CA. You must mail in this CA nonresident state income tax return and include your state W-2 information. You will want to include an explanatory statement with your CA return stating your situation (that your CA employer withheld CA taxes from your wages in error due to a fact that you are a remote working who is a permanent residence of FL).

I would like some additional information please.  I have a similar situation.  I live in FL and work for a company based out of MN; however, I have recently been assigned a traveling position that has me in and out of CA every few weeks.  Am I still required at the end of the year to file a CA state return?  What tax implications should I be aware of?  

Does it matter that I am not living in a permanent residence but rather in a hotel?