So does this mean that I can't use those funds?
You can wait an hope that transaction fees are much lower in the future.
Is there some way to combine all the small transactions into a single large one?
Only by creating a transaction and paying the necessary fee to get the transaction confirmed.
However, if transaction fees happen to get much lower in the future, and you aren't in a hurry for confirmations on the transaction, then you might be able to get a transaction with very low fee transaction confirmed eventually.