My iPad has a protective cover and cannot magnetically connect to my pencil 2. Other options?

A second generation Apple Pencil can only pair and charge via the host iPad’s magnetic/inductive charging dock.

If your protective cover is not designed to permit the Apple Pencil to magnetically dock with your iPad, then the cover is not suitable for use with your iPad.

Many third-party manufacturers of iPad cases do make iPad cases that are designed to accommodate an Apple Pencil. STM and Otterbox are just two examples of manufacturers that do supply cases for various models of iPad/Pencil.

The tags appended to your post suggest that you have an iPad10. The iPad10 is not compatible with the second generation Apple Pencil - but instead supports the first generation Apple Pencil.

The first generation Pencil is charged and paired from an iPad10 using the iPad charging cable - and an Apple USB-C to Apple Pencil Adapter:

New first generation Pencils now ship with this special adapter in the box along with the Pencil. However, some older stock purchased from retailers may lack the USB-C to Lightning adapter - and may instead have an older Lightning to Lightning Adapter.

For owners of older first generation Pencils, or for “old stock” new Pencils, the new special adapter can be purchased directly from Apple as an accessory.

https://store.apple.com/uk/xc/product/MQLU3ZM/A

As such, if purchasing a new first generation Apple Pencil to accompany an iPad10, you might be best advised to visit an Apple Store or Apple Authorised Retailer that has a high-turnover of stock - and ensure that the Pencil box indicates that the correct adapter is included.

If necessary, open the box in the Store and check that the USB-C/Lightning adapter is present - noting that the older Lightning/Lightning adapter looks very similar to the USB-C/Lightning adapter.