Hi Megumi,
There are two different prepositions here, and there is a nuance in their usage.
"in" is often used to indicate location, while "from" is commonly used to indicate a separation of distance or a point of origin.
Therefore, imagine that you are shopping online while at home.
"Now you can enjoy the benefits and convenience of online shopping in the comfort of your home. (Focus is on the fact that you are in your comfortable house.)
Now, imagine that you have a home office and you have the flexibility of working from home (away from your company office) on certain days of the week.
"Now you can enjoy the benefits and flexibility of working from the comfort of your home. (Focus is on the fact that you are away from your company.)
Again, the difference is negligible and native speakers will be able to comprehend either usage.
Hope this helps.
Cheers,
Lance