I'm not sure if you're misunderstanding what VFSTX is compared to a CD, or if you're just a bit loose with your terminology, but:
VFSTX, a mutual fund that holds a set of bonds, does not have an "APY". An APY (annual percentage yield) is a promise that you will receive that return in the future on your investment for the specified period. The numbers you list for VFSTX are simply what it returned in the past. It makes no promises about future returns.
Though it is not common, it is entirely possible that your investment in VFSTX can lose money, which is not possible with an FDIC-insured CD. For example, if you had invested your $10k in 2008, you would have been left with only $9.5k in 2009. On the other hand, if you had held on to it 'til 2009, it would have bounced back up to $10.9k.
It's up to you to decide whether that risk is worth the reward over a CD, which is basically the entire crux of investing.
A short-term bond fund is one of the least-risky non-guaranteed investments you can make, though there are also a whole bunch of other Vanguard short-term bond funds you could select from, all with slightly different risk/reward profiles.