Applications for jobs should always include a cover letter. The cover letter should describe how your experience and education specifically qualify you for the position you are applying for. The person reviewing you application will read the letter to get a basic idea of how you qualify and the use your resume or application to corroborate the letter. Without the letter, you are asking the reviewer to do a lot more work--sometimes that influences the decision about who get an interview.

If you are sending the resume by email, put your letter first and the resume second in the body of the email. It is probably better to not send your resume as an attachment as it might be missed by a casual reviewer.

I have not done any online applications, however I have reviewed many applications for a variety of positions. The letter is important. My guess is that a company that is requesting serious applications will provide a spot for a summary letter in the process--if there is no way to include a summary, specific to that job, you might send them a separate email including you letter, or asking them how to submit a letter of introduction.

There are companies that do the initial review of the applications with a computer program. If they have that many applications and they are so impersonal they don't even take the time to review applications, maybe they are not the best company to work for.

In all cases, make sure the way you present your qualifications is specifically prepared to emphasize how well you could perform in the advertised position--that means a lot to the person reviewing the application. Generic, broad brush applications that are not tailored to the advertised position often go to the bottom of the pile.