It is, but the capital gain is usually taxed in the hands of a beneficiary. The type of beneficiary determines whether the 50% discount applies or not.
ie - if the capital gain is distributed to an individual, the 50% discount applies. If it is distributed to a company, the discount does not apply.
Any income of a trust, whether it be capital gains or ordinary income, is distributed to the beneficiaries and retains the nature of the income without being taxed on the trust. Then the income is taxed on the beneficiaries at their own marginal tax rate, with the 50% discount if they are an individual.